├── .github └── workflows │ └── ci.yml ├── .gitignore ├── CHANGES.txt ├── CODE_OF_CONDUCT.md ├── HOWTOTettelin.txt ├── LICENSE.txt ├── Makefile ├── README.md ├── README.txt ├── TODO.txt ├── _cluster_makeHomolog.pl ├── _cluster_makeInparalog.pl ├── _cluster_makeIsoform.pl ├── _cluster_makeOrtholog.pl ├── _split_blast.pl ├── _split_hmmscan.pl ├── add_pancore_matrices.pl ├── add_pangenome_matrices.pl ├── annotate_cluster.pl ├── bin └── README.txt ├── check_BDBHs.pl ├── compare_clusters.pl ├── cpanfile ├── db └── README.txt ├── docker └── Dockerfile ├── download_genomes_ncbi.pl ├── get_homologues-est.pl ├── get_homologues.pl ├── hcluster_pangenome_matrix.sh ├── install.pl ├── lib ├── ForkManager.pm ├── HPCluster.pm ├── bioperl-1.5.2_102 │ ├── AUTHORS │ ├── Bio │ │ ├── AnnotatableI.pm │ │ ├── Annotation │ │ │ ├── AnnotationFactory.pm │ │ │ ├── Collection.pm │ │ │ ├── Comment.pm │ │ │ ├── DBLink.pm │ │ │ ├── OntologyTerm.pm │ │ │ ├── Reference.pm │ │ │ ├── SimpleValue.pm │ │ │ ├── StructuredValue.pm │ │ │ ├── Target.pm │ │ │ └── TypeManager.pm │ │ ├── AnnotationCollectionI.pm │ │ ├── AnnotationI.pm │ │ ├── Coordinate │ │ │ ├── Chain.pm │ │ │ ├── Collection.pm │ │ │ ├── ExtrapolatingPair.pm │ │ │ ├── GeneMapper.pm │ │ │ ├── Graph.pm │ │ │ ├── MapperI.pm │ │ │ ├── Pair.pm │ │ │ ├── Result.pm │ │ │ ├── Result │ │ │ │ ├── Gap.pm │ │ │ │ └── Match.pm │ │ │ ├── ResultI.pm │ │ │ └── Utils.pm │ │ ├── DB │ │ │ ├── Taxonomy.pm │ │ │ ├── Taxonomy │ │ │ │ ├── entrez.pm │ │ │ │ ├── flatfile.pm │ │ │ │ └── list.pm │ │ │ └── WebDBSeqI.pm │ │ ├── DescribableI.pm │ │ ├── Factory │ │ │ ├── AnalysisI.pm │ │ │ ├── ApplicationFactoryI.pm │ │ │ ├── DriverFactory.pm │ │ │ ├── FTLocationFactory.pm │ │ │ ├── HitFactoryI.pm │ │ │ ├── LocationFactoryI.pm │ │ │ ├── MapFactoryI.pm │ │ │ ├── ObjectBuilderI.pm │ │ │ ├── ObjectFactory.pm │ │ │ ├── ObjectFactoryI.pm │ │ │ ├── ResultFactoryI.pm │ │ │ ├── SeqAnalysisParserFactory.pm │ │ │ ├── SeqAnalysisParserFactoryI.pm │ │ │ ├── SequenceFactoryI.pm │ │ │ ├── SequenceProcessorI.pm │ │ │ ├── SequenceStreamI.pm │ │ │ └── TreeFactoryI.pm │ │ ├── FeatureHolderI.pm │ │ ├── Graph │ │ │ ├── Edge.pm │ │ │ ├── IO.pm │ │ │ ├── IO │ │ │ │ ├── dip.pm │ │ │ │ └── psi_xml.pm │ │ │ ├── ProteinGraph.pm │ │ │ ├── SimpleGraph.pm │ │ │ └── SimpleGraph │ │ │ │ └── Traversal.pm │ │ ├── Graphics.pm │ │ ├── Graphics │ │ │ ├── ConfiguratorI.pm │ │ │ ├── Feature.pm │ │ │ ├── FeatureBase.pm │ │ │ ├── FeatureFile.pm │ │ │ ├── FeatureFile │ │ │ │ └── Iterator.pm │ │ │ ├── Glyph.pm │ │ │ ├── Glyph │ │ │ │ ├── Factory.pm │ │ │ │ ├── alignment.pm │ │ │ │ ├── anchored_arrow.pm │ │ │ │ ├── arrow.pm │ │ │ │ ├── box.pm │ │ │ │ ├── broken_line.pm │ │ │ │ ├── cds.pm │ │ │ │ ├── christmas_arrow.pm │ │ │ │ ├── crossbox.pm │ │ │ │ ├── dashed_line.pm │ │ │ │ ├── diamond.pm │ │ │ │ ├── dna.pm │ │ │ │ ├── dot.pm │ │ │ │ ├── dumbbell.pm │ │ │ │ ├── ellipse.pm │ │ │ │ ├── ex.pm │ │ │ │ ├── extending_arrow.pm │ │ │ │ ├── flag.pm │ │ │ │ ├── gene.pm │ │ │ │ ├── generic.pm │ │ │ │ ├── graded_segments.pm │ │ │ │ ├── group.pm │ │ │ │ ├── heterogeneous_segments.pm │ │ │ │ ├── image.pm │ │ │ │ ├── lightning.pm │ │ │ │ ├── line.pm │ │ │ │ ├── merge_parts.pm │ │ │ │ ├── merged_alignment.pm │ │ │ │ ├── minmax.pm │ │ │ │ ├── oval.pm │ │ │ │ ├── pentagram.pm │ │ │ │ ├── pinsertion.pm │ │ │ │ ├── primers.pm │ │ │ │ ├── processed_transcript.pm │ │ │ │ ├── protein.pm │ │ │ │ ├── ragged_ends.pm │ │ │ │ ├── redgreen_box.pm │ │ │ │ ├── redgreen_segment.pm │ │ │ │ ├── repeating_shape.pm │ │ │ │ ├── rndrect.pm │ │ │ │ ├── ruler_arrow.pm │ │ │ │ ├── saw_teeth.pm │ │ │ │ ├── segmented_keyglyph.pm │ │ │ │ ├── segments.pm │ │ │ │ ├── so_transcript.pm │ │ │ │ ├── span.pm │ │ │ │ ├── splice_site.pm │ │ │ │ ├── text_in_box.pm │ │ │ │ ├── three_letters.pm │ │ │ │ ├── tic_tac_toe.pm │ │ │ │ ├── toomany.pm │ │ │ │ ├── track.pm │ │ │ │ ├── transcript.pm │ │ │ │ ├── transcript2.pm │ │ │ │ ├── translation.pm │ │ │ │ ├── triangle.pm │ │ │ │ ├── two_bolts.pm │ │ │ │ ├── wave.pm │ │ │ │ ├── weighted_arrow.pm │ │ │ │ ├── whiskerplot.pm │ │ │ │ └── xyplot.pm │ │ │ ├── Panel.pm │ │ │ ├── Pictogram.pm │ │ │ ├── RendererI.pm │ │ │ └── Util.pm │ │ ├── IdentifiableI.pm │ │ ├── LocatableSeq.pm │ │ ├── Location │ │ │ ├── Atomic.pm │ │ │ ├── AvWithinCoordPolicy.pm │ │ │ ├── CoordinatePolicyI.pm │ │ │ ├── Fuzzy.pm │ │ │ ├── FuzzyLocationI.pm │ │ │ ├── NarrowestCoordPolicy.pm │ │ │ ├── Simple.pm │ │ │ ├── Split.pm │ │ │ ├── SplitLocationI.pm │ │ │ └── WidestCoordPolicy.pm │ │ ├── LocationI.pm │ │ ├── Perl.pm │ │ ├── PrimarySeq.pm │ │ ├── PrimarySeqI.pm │ │ ├── README │ │ ├── Range.pm │ │ ├── RangeI.pm │ │ ├── Root │ │ │ ├── Exception.pm │ │ │ ├── HTTPget.pm │ │ │ ├── IO.pm │ │ │ ├── Root.pm │ │ │ ├── RootI.pm │ │ │ ├── Storable.pm │ │ │ └── Version.pm │ │ ├── Seq.pm │ │ ├── Seq │ │ │ ├── BaseSeqProcessor.pm │ │ │ ├── EncodedSeq.pm │ │ │ ├── LargeLocatableSeq.pm │ │ │ ├── LargePrimarySeq.pm │ │ │ ├── LargeSeq.pm │ │ │ ├── LargeSeqI.pm │ │ │ ├── Meta.pm │ │ │ ├── Meta │ │ │ │ └── Array.pm │ │ │ ├── MetaI.pm │ │ │ ├── PrimaryQual.pm │ │ │ ├── PrimedSeq.pm │ │ │ ├── QualI.pm │ │ │ ├── Quality.pm │ │ │ ├── RichSeq.pm │ │ │ ├── RichSeqI.pm │ │ │ ├── SeqBuilder.pm │ │ │ ├── SeqFactory.pm │ │ │ ├── SeqFastaSpeedFactory.pm │ │ │ ├── SeqWithQuality.pm │ │ │ ├── SequenceTrace.pm │ │ │ └── TraceI.pm │ │ ├── SeqAnalysisParserI.pm │ │ ├── SeqFeature │ │ │ ├── Annotated.pm │ │ │ ├── AnnotationAdaptor.pm │ │ │ ├── Collection.pm │ │ │ ├── CollectionI.pm │ │ │ ├── Computation.pm │ │ │ ├── FeaturePair.pm │ │ │ ├── Gene │ │ │ │ ├── Exon.pm │ │ │ │ ├── ExonI.pm │ │ │ │ ├── GeneStructure.pm │ │ │ │ ├── GeneStructureI.pm │ │ │ │ ├── Intron.pm │ │ │ │ ├── NC_Feature.pm │ │ │ │ ├── Poly_A_site.pm │ │ │ │ ├── Promoter.pm │ │ │ │ ├── Transcript.pm │ │ │ │ ├── TranscriptI.pm │ │ │ │ └── UTR.pm │ │ │ ├── Generic.pm │ │ │ ├── PositionProxy.pm │ │ │ ├── Primer.pm │ │ │ ├── SiRNA │ │ │ │ ├── Oligo.pm │ │ │ │ └── Pair.pm │ │ │ ├── Similarity.pm │ │ │ ├── SimilarityPair.pm │ │ │ ├── Tools │ │ │ │ ├── FeatureNamer.pm │ │ │ │ ├── IDHandler.pm │ │ │ │ ├── TypeMapper.pm │ │ │ │ └── Unflattener.pm │ │ │ └── TypedSeqFeatureI.pm │ │ ├── SeqFeatureI.pm │ │ ├── SeqI.pm │ │ ├── SeqIO.pm │ │ ├── SeqIO │ │ │ ├── FTHelper.pm │ │ │ ├── MultiFile.pm │ │ │ ├── abi.pm │ │ │ ├── ace.pm │ │ │ ├── agave.pm │ │ │ ├── alf.pm │ │ │ ├── asciitree.pm │ │ │ ├── bsml.pm │ │ │ ├── bsml_sax.pm │ │ │ ├── chadoxml.pm │ │ │ ├── chaos.pm │ │ │ ├── chaosxml.pm │ │ │ ├── ctf.pm │ │ │ ├── embl.pm │ │ │ ├── entrezgene.pm │ │ │ ├── excel.pm │ │ │ ├── exp.pm │ │ │ ├── fasta.pm │ │ │ ├── fastq.pm │ │ │ ├── game.pm │ │ │ ├── game │ │ │ │ ├── featHandler.pm │ │ │ │ ├── gameHandler.pm │ │ │ │ ├── gameSubs.pm │ │ │ │ ├── gameWriter.pm │ │ │ │ └── seqHandler.pm │ │ │ ├── gcg.pm │ │ │ ├── genbank.pm │ │ │ ├── interpro.pm │ │ │ ├── kegg.pm │ │ │ ├── largefasta.pm │ │ │ ├── lasergene.pm │ │ │ ├── locuslink.pm │ │ │ ├── metafasta.pm │ │ │ ├── phd.pm │ │ │ ├── pir.pm │ │ │ ├── pln.pm │ │ │ ├── qual.pm │ │ │ ├── raw.pm │ │ │ ├── scf.pm │ │ │ ├── strider.pm │ │ │ ├── swiss.pm │ │ │ ├── tab.pm │ │ │ ├── table.pm │ │ │ ├── tigr.pm │ │ │ ├── tigrxml.pm │ │ │ ├── tinyseq.pm │ │ │ ├── tinyseq │ │ │ │ └── tinyseqHandler.pm │ │ │ └── ztr.pm │ │ ├── SeqUtils.pm │ │ ├── Species.pm │ │ ├── Taxon.pm │ │ ├── Tools │ │ │ ├── CodonTable.pm │ │ │ ├── GFF.pm │ │ │ ├── GuessSeqFormat.pm │ │ │ └── IUPAC.pm │ │ └── Tree │ │ │ ├── AlleleNode.pm │ │ │ ├── Compatible.pm │ │ │ ├── DistanceFactory.pm │ │ │ ├── Draw │ │ │ └── Cladogram.pm │ │ │ ├── Node.pm │ │ │ ├── NodeI.pm │ │ │ ├── NodeNHX.pm │ │ │ ├── RandomFactory.pm │ │ │ ├── Statistics.pm │ │ │ ├── Tree.pm │ │ │ ├── TreeFunctionsI.pm │ │ │ └── TreeI.pm │ ├── LICENSE │ ├── README │ └── README2 ├── est │ ├── TransDecoder_r20140704 │ │ ├── LICENSE.txt │ │ ├── PerlLib │ │ │ ├── Fasta_reader.pm │ │ │ ├── GFF3_utils.pm │ │ │ ├── Gene_obj.pm │ │ │ ├── Gene_obj_indexer.pm │ │ │ ├── Longest_orf.pm │ │ │ ├── Nuc_translator.pm │ │ │ ├── TiedHash.pm │ │ │ └── URI │ │ │ │ └── Escape.pm │ │ ├── README │ │ ├── TransDecoder │ │ └── util │ │ │ ├── compute_base_probs.pl │ │ │ ├── gene_list_to_gff.pl │ │ │ ├── get_top_longest_fasta_entries.pl │ │ │ ├── gff3_file_to_bed.pl │ │ │ ├── gff3_file_to_proteins.pl │ │ │ ├── index_gff3_files_by_isoform.pl │ │ │ ├── nr_ORFs_gff3.pl │ │ │ ├── remove_eclipsed_ORFs.pl │ │ │ ├── score_CDS_liklihood_all_6_frames.pl │ │ │ └── seq_n_baseprobs_to_logliklihood_vals.pl │ ├── cppcode.pm │ └── transcripts.pm ├── marfil_homology.pm ├── mview │ ├── CHANGES │ ├── LICENSE.md │ ├── Makefile │ ├── Makefile.PL │ ├── README.md │ ├── bin │ │ ├── Makefile │ │ └── mview │ ├── doc │ │ ├── Sphinx │ │ │ ├── Makefile │ │ │ ├── build │ │ │ │ └── html │ │ │ │ │ ├── .buildinfo │ │ │ │ │ ├── .nojekyll │ │ │ │ │ ├── _sources │ │ │ │ │ ├── contents.rst.txt │ │ │ │ │ ├── contents.txt │ │ │ │ │ ├── etc │ │ │ │ │ │ ├── Licence.rst.txt │ │ │ │ │ │ └── Licence.txt │ │ │ │ │ ├── index.rst.txt │ │ │ │ │ ├── index.txt │ │ │ │ │ ├── install │ │ │ │ │ │ ├── module.rst.txt │ │ │ │ │ │ ├── perl.rst.txt │ │ │ │ │ │ ├── unix.rst.txt │ │ │ │ │ │ └── windows.rst.txt │ │ │ │ │ └── manual │ │ │ │ │ │ ├── blast │ │ │ │ │ │ ├── blast1.rst.txt │ │ │ │ │ │ ├── blast1.txt │ │ │ │ │ │ ├── blast2.rst.txt │ │ │ │ │ │ ├── blast2.txt │ │ │ │ │ │ ├── rules.rst.txt │ │ │ │ │ │ └── rules.txt │ │ │ │ │ │ ├── faq.rst.txt │ │ │ │ │ │ ├── faq.txt │ │ │ │ │ │ ├── formats_in.rst.txt │ │ │ │ │ │ ├── formats_in.txt │ │ │ │ │ │ ├── formats_out.rst.txt │ │ │ │ │ │ ├── formats_out.txt │ │ │ │ │ │ ├── intro.txt │ │ │ │ │ │ ├── manual.rst.txt │ │ │ │ │ │ └── manual.txt │ │ │ │ │ ├── _static │ │ │ │ │ ├── MView.css │ │ │ │ │ ├── ajax-loader.gif │ │ │ │ │ ├── basic.css │ │ │ │ │ ├── comment-bright.png │ │ │ │ │ ├── comment-close.png │ │ │ │ │ ├── comment.png │ │ │ │ │ ├── contents.png │ │ │ │ │ ├── doctools.js │ │ │ │ │ ├── down-pressed.png │ │ │ │ │ ├── down.png │ │ │ │ │ ├── file.png │ │ │ │ │ ├── jquery-3.1.0.js │ │ │ │ │ ├── jquery.js │ │ │ │ │ ├── minus.png │ │ │ │ │ ├── navigation.png │ │ │ │ │ ├── plus.png │ │ │ │ │ ├── pygments.css │ │ │ │ │ ├── searchtools.js │ │ │ │ │ ├── sphinxdoc.css │ │ │ │ │ ├── underscore-1.3.1.js │ │ │ │ │ ├── underscore.js │ │ │ │ │ ├── up-pressed.png │ │ │ │ │ ├── up.png │ │ │ │ │ └── websupport.js │ │ │ │ │ ├── contents.html │ │ │ │ │ ├── etc │ │ │ │ │ └── Licence.html │ │ │ │ │ ├── genindex.html │ │ │ │ │ ├── index.html │ │ │ │ │ ├── manual │ │ │ │ │ ├── blast │ │ │ │ │ │ ├── blast1.html │ │ │ │ │ │ ├── blast2.html │ │ │ │ │ │ └── rules.html │ │ │ │ │ ├── faq.html │ │ │ │ │ ├── formats_in.html │ │ │ │ │ ├── formats_out.html │ │ │ │ │ ├── intro.html │ │ │ │ │ └── manual.html │ │ │ │ │ ├── objects.inv │ │ │ │ │ ├── search.html │ │ │ │ │ └── searchindex.js │ │ │ └── source │ │ │ │ ├── _static │ │ │ │ └── MView.css │ │ │ │ ├── conf.py │ │ │ │ ├── contents.rst │ │ │ │ ├── etc │ │ │ │ └── Licence.rst │ │ │ │ ├── index.rst │ │ │ │ ├── install │ │ │ │ ├── perl.rst │ │ │ │ ├── unix.rst │ │ │ │ └── windows.rst │ │ │ │ └── manual │ │ │ │ ├── blast │ │ │ │ ├── blast1.rst │ │ │ │ ├── blast2.rst │ │ │ │ └── rules.rst │ │ │ │ ├── faq.rst │ │ │ │ ├── formats_in.rst │ │ │ │ ├── formats_out.rst │ │ │ │ ├── intro.rst │ │ │ │ ├── manual.rst │ │ │ │ └── unused.txt │ │ ├── data │ │ │ ├── MAKE_FIGURES │ │ │ ├── blastn.dat │ │ │ ├── clustal.dat │ │ │ ├── commented.dat │ │ │ ├── data.dat │ │ │ ├── data_ncbi_id.dat │ │ │ ├── data_srs.dat │ │ │ ├── data_sw_id.dat │ │ │ ├── dssp.dat │ │ │ ├── listcolors │ │ │ ├── listcss │ │ │ └── listgroups │ │ └── html │ ├── etc │ │ ├── COPYRIGHT.templ │ │ ├── MAKEFILE.templ │ │ └── Makefile.example │ ├── install.pl │ ├── lib │ │ ├── Bio │ │ │ ├── MView │ │ │ │ ├── Align.pm │ │ │ │ ├── Align │ │ │ │ │ ├── Alignment.pm │ │ │ │ │ ├── ColorMixin.pm │ │ │ │ │ ├── Consensus.pm │ │ │ │ │ ├── Conservation.pm │ │ │ │ │ ├── Header.pm │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Row.pm │ │ │ │ │ ├── Ruler.pm │ │ │ │ │ ├── Sequence.pm │ │ │ │ │ └── Special.pm │ │ │ │ ├── Build.pm │ │ │ │ ├── Build │ │ │ │ │ ├── Align.pm │ │ │ │ │ ├── Base.pm │ │ │ │ │ ├── Format │ │ │ │ │ │ ├── BLAST.pm │ │ │ │ │ │ ├── BLAST0.pm │ │ │ │ │ │ ├── BLAST1.pm │ │ │ │ │ │ ├── BLAST2.pm │ │ │ │ │ │ ├── CLUSTAL.pm │ │ │ │ │ │ ├── FASTA.pm │ │ │ │ │ │ ├── FASTA1.pm │ │ │ │ │ │ ├── FASTA2.pm │ │ │ │ │ │ ├── FASTA3.pm │ │ │ │ │ │ ├── FASTA3X.pm │ │ │ │ │ │ ├── HSSP.pm │ │ │ │ │ │ ├── JNETZ.pm │ │ │ │ │ │ ├── MAF.pm │ │ │ │ │ │ ├── MIPS.pm │ │ │ │ │ │ ├── MSF.pm │ │ │ │ │ │ ├── MULTAS.pm │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── PIR.pm │ │ │ │ │ │ ├── Pearson.pm │ │ │ │ │ │ └── Plain.pm │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Row.pm │ │ │ │ │ ├── RowInfoMixin.pm │ │ │ │ │ ├── Scheduler.pm │ │ │ │ │ └── Search.pm │ │ │ │ ├── Color │ │ │ │ │ ├── ColorMap.pm │ │ │ │ │ ├── Makefile │ │ │ │ │ └── Palette.pm │ │ │ │ ├── Convert.pm │ │ │ │ ├── Display.pm │ │ │ │ ├── Display │ │ │ │ │ ├── Any.pm │ │ │ │ │ ├── Display.pm │ │ │ │ │ ├── Header.pm │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Out │ │ │ │ │ │ ├── HTML.pm │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ └── Text.pm │ │ │ │ │ ├── Panel.pm │ │ │ │ │ ├── Ruler.pm │ │ │ │ │ ├── Sequence.pm │ │ │ │ │ └── Track.pm │ │ │ │ ├── GroupMap.pm │ │ │ │ ├── Makefile │ │ │ │ ├── Manager.pm │ │ │ │ ├── Option │ │ │ │ │ ├── Arguments.pm │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── Options.pm │ │ │ │ │ ├── Parameters.pm │ │ │ │ │ ├── Parser.pm │ │ │ │ │ └── Types.pm │ │ │ │ ├── SRS.pm │ │ │ │ ├── Sequence.pm │ │ │ │ └── Sequence │ │ │ │ │ ├── Base.pm │ │ │ │ │ ├── Forward.pm │ │ │ │ │ ├── Makefile │ │ │ │ │ └── Reverse.pm │ │ │ ├── Makefile │ │ │ ├── Parse │ │ │ │ ├── Block.pm │ │ │ │ ├── BlockKeeper.pm │ │ │ │ ├── Format │ │ │ │ │ ├── BLAST.pm │ │ │ │ │ ├── BLAST1.pm │ │ │ │ │ ├── BLAST1 │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── blastn.pm │ │ │ │ │ │ ├── blastp.pm │ │ │ │ │ │ ├── blastx.pm │ │ │ │ │ │ ├── tblastn.pm │ │ │ │ │ │ └── tblastx.pm │ │ │ │ │ ├── BLAST2.pm │ │ │ │ │ ├── BLAST2 │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── blastn.pm │ │ │ │ │ │ ├── blastp.pm │ │ │ │ │ │ ├── blastx.pm │ │ │ │ │ │ ├── tblastn.pm │ │ │ │ │ │ └── tblastx.pm │ │ │ │ │ ├── BLAST2_OF7.pm │ │ │ │ │ ├── BLAST2_OF7 │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── blastn.pm │ │ │ │ │ │ ├── blastp.pm │ │ │ │ │ │ ├── blastx.pm │ │ │ │ │ │ ├── tblastn.pm │ │ │ │ │ │ └── tblastx.pm │ │ │ │ │ ├── CLUSTAL.pm │ │ │ │ │ ├── FASTA.pm │ │ │ │ │ ├── FASTA1.pm │ │ │ │ │ ├── FASTA1 │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ └── fasta.pm │ │ │ │ │ ├── FASTA2.pm │ │ │ │ │ ├── FASTA2 │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── align.pm │ │ │ │ │ │ ├── fasta.pm │ │ │ │ │ │ ├── lalign.pm │ │ │ │ │ │ ├── ssearch.pm │ │ │ │ │ │ └── tfasta.pm │ │ │ │ │ ├── FASTA2_GCG.pm │ │ │ │ │ ├── FASTA2_GCG │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ └── fasta.pm │ │ │ │ │ ├── FASTA3.pm │ │ │ │ │ ├── FASTA3 │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── fasta.pm │ │ │ │ │ │ ├── fastx.pm │ │ │ │ │ │ └── tfasta.pm │ │ │ │ │ ├── FASTA3X.pm │ │ │ │ │ ├── FASTA3X │ │ │ │ │ │ ├── Makefile │ │ │ │ │ │ ├── fasta.pm │ │ │ │ │ │ ├── fastm.pm │ │ │ │ │ │ ├── fastx.pm │ │ │ │ │ │ ├── ggsearch.pm │ │ │ │ │ │ ├── glsearch.pm │ │ │ │ │ │ ├── ssearch.pm │ │ │ │ │ │ ├── tfasta.pm │ │ │ │ │ │ └── tfastm.pm │ │ │ │ │ ├── HSSP.pm │ │ │ │ │ ├── JNETZ.pm │ │ │ │ │ ├── MAF.pm │ │ │ │ │ ├── MIPS.pm │ │ │ │ │ ├── MSF.pm │ │ │ │ │ ├── MULTAS.pm │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── PIR.pm │ │ │ │ │ ├── Pearson.pm │ │ │ │ │ └── Plain.pm │ │ │ │ ├── Makefile │ │ │ │ ├── ReadFile.pm │ │ │ │ ├── ReadText.pm │ │ │ │ ├── Record.pm │ │ │ │ ├── Scanner.pm │ │ │ │ ├── Stream.pm │ │ │ │ └── Strings.pm │ │ │ ├── SRS.pm │ │ │ └── Util │ │ │ │ ├── File.pm │ │ │ │ ├── Makefile │ │ │ │ ├── Math.pm │ │ │ │ ├── Object.pm │ │ │ │ ├── Regexp.pm │ │ │ │ └── System.pm │ │ ├── Getopt.pm │ │ ├── Makefile │ │ ├── NPB │ │ │ ├── Makefile │ │ │ └── Parse │ │ │ │ ├── Format │ │ │ │ ├── BLAST.pm │ │ │ │ ├── BLAST1.pm │ │ │ │ ├── BLAST1 │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── blastn.pm │ │ │ │ │ ├── blastp.pm │ │ │ │ │ ├── blastx.pm │ │ │ │ │ ├── tblastn.pm │ │ │ │ │ └── tblastx.pm │ │ │ │ ├── BLAST2.pm │ │ │ │ ├── BLAST2 │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── blastn.pm │ │ │ │ │ ├── blastp.pm │ │ │ │ │ ├── blastx.pm │ │ │ │ │ ├── tblastn.pm │ │ │ │ │ └── tblastx.pm │ │ │ │ ├── BLAST2_OF7.pm │ │ │ │ ├── BLAST2_OF7 │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── blastn.pm │ │ │ │ │ ├── blastp.pm │ │ │ │ │ ├── blastx.pm │ │ │ │ │ ├── tblastn.pm │ │ │ │ │ └── tblastx.pm │ │ │ │ ├── BLOCKS.pm │ │ │ │ ├── CLUSTAL.pm │ │ │ │ ├── FASTA.pm │ │ │ │ ├── FASTA1.pm │ │ │ │ ├── FASTA1 │ │ │ │ │ ├── Makefile │ │ │ │ │ └── fasta.pm │ │ │ │ ├── FASTA2.pm │ │ │ │ ├── FASTA2 │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── align.pm │ │ │ │ │ ├── fasta.pm │ │ │ │ │ ├── lalign.pm │ │ │ │ │ ├── ssearch.pm │ │ │ │ │ └── tfasta.pm │ │ │ │ ├── FASTA3.pm │ │ │ │ ├── FASTA3 │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── fasta.pm │ │ │ │ │ ├── fastx.pm │ │ │ │ │ └── tfasta.pm │ │ │ │ ├── FASTA3X.pm │ │ │ │ ├── FASTA3X │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── fasta.pm │ │ │ │ │ ├── fastm.pm │ │ │ │ │ ├── fastx.pm │ │ │ │ │ ├── ggsearch.pm │ │ │ │ │ ├── glsearch.pm │ │ │ │ │ ├── ssearch.pm │ │ │ │ │ ├── tfasta.pm │ │ │ │ │ └── tfastm.pm │ │ │ │ ├── GCG_FASTA2.pm │ │ │ │ ├── GCG_FASTA2 │ │ │ │ │ ├── Makefile │ │ │ │ │ └── fasta.pm │ │ │ │ ├── HSSP.pm │ │ │ │ ├── JNETZ.pm │ │ │ │ ├── MAF.pm │ │ │ │ ├── MIPS.pm │ │ │ │ ├── MSF.pm │ │ │ │ ├── MULTAS.pm │ │ │ │ ├── Makefile │ │ │ │ ├── PIR.pm │ │ │ │ ├── Pearson.pm │ │ │ │ ├── Plain.pm │ │ │ │ ├── Slurp.pm │ │ │ │ └── attic │ │ │ │ │ ├── EMBL.pm │ │ │ │ │ ├── FT.pm │ │ │ │ │ ├── Genbank.pm │ │ │ │ │ └── SIM.pm │ │ │ │ ├── Makefile │ │ │ │ ├── Math.pm │ │ │ │ ├── Message.pm │ │ │ │ ├── Record.pm │ │ │ │ ├── Regexps.pm │ │ │ │ ├── Stream.pm │ │ │ │ ├── Substring.pm │ │ │ │ └── attic │ │ │ │ └── Index.pm │ │ └── Universal.pm │ └── t │ │ └── test_Bio::MView::Sequence.pl └── phyTools.pm ├── make_nr_pangenome_matrix.pl ├── manual_get_homologues-est.pdf ├── manual_get_homologues.pdf ├── pangenome_tutorial.html ├── parse_pangenome_matrix.pl ├── pfam_enrich.pl ├── pics ├── EST.jpg ├── logoARAID.gif ├── logoCSIC.png ├── logoELIXIRES.png ├── logoUNAM.png └── summary.jpg ├── plot_matrix_heatmap.sh ├── plot_pancore_matrix.pl ├── sample.HPC.conf ├── sample_buch_fasta ├── Buch_aph_APS.faa ├── Buch_aph_Bp.faa ├── Buch_aph_Cc.faa └── Buch_aphid_Sg.faa ├── sample_cluster.fna ├── sample_intersection ├── 10_mrx.faa ├── 11_blaCTX-M-1.faa ├── 13_hypothetical_protein.faa ├── 159_intI1.faa ├── 160_oxa2.faa ├── 163_unknown.faa ├── 166_unknown.faa ├── 168_unknown.faa ├── 170_tetA.faa ├── 171_unknown.faa ├── 172_unknown.faa ├── 173_arsR.faa ├── 174_arsD.faa ├── 175_arsA.faa ├── 176_arsB.faa ├── 177_arsC.faa ├── 198_TnpA.faa ├── 200_AacA4.faa ├── 201_VIM-1.faa ├── 225_delta-FipA.faa ├── 226_TnpA.faa ├── 228_truncated_TnpA.faa ├── 229_QnrS1.faa ├── 230_hypothetical_protein.faa ├── 231_hypothetical_protein.faa ├── 232_hypothetical_protein.faa ├── 233_YdaA.faa ├── 234_hypothetical_protein.faa ├── 235_hypothetical_protein.faa ├── 236_putative_DeoR-type_t...faa ├── 238_TnpA.faa ├── 240_putative_invertase-r...faa ├── 241_PilT.faa ├── 242_TnpA.faa ├── 243_TnpM.faa ├── 245_dfrA14.faa ├── 246_hypothetical_protein.faa ├── 250_putative_mobilizatio...faa ├── 253_transposition_modula...faa ├── 255_hypothetical_protein.faa ├── 264_hypothetical_protein.faa ├── 268_hypothetical_protein.faa ├── 279_transposase.faa ├── 280_transposase.faa ├── 281_phage_integrase_fami...faa ├── 282_hypothetical_protein.faa ├── 286_streptomycin_phospho...faa ├── 288_resolvase.faa ├── 289_beta-lactamase.faa ├── 293_hypothetical_protein.faa ├── 294_hypothetical_protein.faa ├── 295_hypothetical_protein.faa ├── 296_hypothetical_protein.faa ├── 297_hypothetical_protein.faa ├── 298_conserved_hypothetic...faa ├── 299_site-specific_recomb...faa ├── 301_putative_transposase.faa ├── 302_conserved_hypothetic...faa ├── 304_transposase-_IS4_fam...faa ├── 305_transposase.faa ├── 307_hypothetical_protein.faa ├── 308_conserved_hypothetic...faa ├── 318_TraB.faa ├── 321_arsenical_pump-drivi...faa ├── 327_TraB.faa ├── 338_InsB.faa ├── 341_hypothetical_protein.faa ├── 348_group_II_intron-enco...faa ├── 349_transposase_InsF.faa ├── 34_methyl-accepting_che...faa ├── 350_transposase.faa ├── 351_putative_transposase...faa ├── 352_resolvase.faa ├── 353_S-formylglutathione_...faa ├── 354_glyoxalase-bleomycin...faa ├── 355_S--hydroxymethyl-glu...faa ├── 35_tnpA.faa ├── 362_group_II_intron-enco...faa ├── 363_putative_transposase...faa ├── 364_conserved_hypothetic...faa ├── 365_NADH_dehydrogenase-_...faa ├── 366_excinuclease_ABC-_A_...faa ├── 367_ISEc8_transposase.faa ├── 368_hypothetical_protein.faa ├── 36_beta-lactamase_CTX-M...faa ├── 376_hypothetical_protein.faa ├── 379_hypothetical_protein.faa ├── 380_hypothetical_protein.faa ├── 381_hypothetical_protein.faa ├── 382_conserved_hypothetic...faa ├── 383_hypothetical_protein.faa ├── 384_hypothetical_protein.faa ├── 390_hypothetical_protein.faa ├── 391_hypothetical_protein.faa ├── 396_TraK.faa ├── 400_DNA_polymerase-_beta...faa ├── 401_protein_of_unknown_f...faa ├── 402_conserved_hypothetic...faa ├── 408_hypothetical_protein.faa ├── 413_TraA.faa ├── 416_TraL.faa ├── 417_hypothetical_protein.faa ├── 420_hypothetical_protein.faa ├── 434_qnrA1.faa ├── 435_ampR.faa ├── 438_unknown.faa ├── 444_FosA.faa ├── 445_tnpA.faa ├── 448_hypothetical_protein.faa ├── 471_putative_relaxase-he...faa ├── 495_MAK2.05.faa ├── 497_ble.faa ├── 498_sph.faa ├── 501_yahA.faa ├── 523_pecM.faa ├── 528_MAK2.40.faa ├── 547_insA.faa ├── 548_insB.faa ├── 557_insF.faa ├── 601_repA.faa ├── 602_resP.faa ├── 603_ecoRII.faa ├── 604_dcm.faa ├── 605_hypothetical_protein.faa ├── 606_type_IV_restriction_...faa ├── 607_tetC.faa ├── 608_tetB.faa ├── 609_tetR.faa ├── 60_ant39.faa ├── 611_strB.faa ├── 613_kikA.faa ├── 614_hypothetical_protein.faa ├── 615_korB.faa ├── 616_traL.faa ├── 617_korA.faa ├── 618_traM.faa ├── 619_traA.faa ├── 61_linF.faa ├── 620_traB.faa ├── 621_traC.faa ├── 622_eex.faa ├── 623_traD.faa ├── 624_traN.faa ├── 625_traE.faa ├── 626_traO.faa ├── 627_traF.faa ├── 628_traG.faa ├── 629_nuc.faa ├── 630_fipA.faa ├── 631_traI.faa ├── 632_traJ.faa ├── 633_traK.faa ├── 634_stbA.faa ├── 635_stbB.faa ├── 636_stbC.faa ├── 637_hypothetical_protein.faa ├── 638_ccgAII.faa ├── 639_ccgAI.faa ├── 640_ardA.faa ├── 641_ccgC.faa ├── 642_ccgD.faa ├── 643_ccgEIII.faa ├── 644_ardR.faa ├── 645_ardB.faa ├── 646_mucA.faa ├── 647_mucB.faa ├── 648_mpr.faa ├── 649_ardK.faa ├── 64_qacEdelta1.faa ├── 65_sul1.faa ├── 66_hypothetical_protein.faa ├── 68_armA.faa ├── 69_hypothetical_protein.faa ├── 70_tnpD.faa ├── 71_mel.faa ├── 72_mph1.faa ├── 73_mph2.faa ├── 743_putative_IS91_ORF2.faa ├── 744_tnp.faa ├── 74_hypothetical_protein.faa ├── 7_transposase_A.faa ├── 87_traA.faa ├── 8_tnpA.faa ├── 9_mphA.faa ├── intersection_t0.cluster_list ├── pangenome_matrix_genes_t0.tab ├── pangenome_matrix_genes_t0.tr.tab ├── pangenome_matrix_t0.fasta ├── pangenome_matrix_t0.phylip ├── pangenome_matrix_t0.tab ├── pangenome_matrix_t0.tabed ├── pangenome_matrix_t0.tr.csv ├── pangenome_matrix_t0.tr.tab ├── pangenome_matrix_t0_KlebsiellaoxytocaKOX105_cloud_list.txt ├── pangenome_matrix_t0_KlebsiellaoxytocaKOX105_core_list.txt ├── pangenome_matrix_t0_KlebsiellaoxytocaKOX105_pangenes_list.txt ├── pangenome_matrix_t0_KlebsiellaoxytocaKOX105_shell.pdf ├── pangenome_matrix_t0_KlebsiellaoxytocaKOX105_shell_circle.pdf ├── pangenome_matrix_t0_KlebsiellaoxytocaKOX105_shell_estimates.tab ├── pangenome_matrix_t0_KlebsiellaoxytocaKOX105_shell_input.txt ├── pangenome_matrix_t0_KlebsiellaoxytocaKOX105_shell_list.txt ├── pangenome_matrix_t0_KlebsiellaoxytocaKOX105_softcore_list.txt ├── pangenome_matrix_t0__cloud_list.txt ├── pangenome_matrix_t0__core_list.txt ├── pangenome_matrix_t0__shell.pdf ├── pangenome_matrix_t0__shell_circle.pdf ├── pangenome_matrix_t0__shell_estimates.tab ├── pangenome_matrix_t0__shell_input.txt ├── pangenome_matrix_t0__shell_list.txt ├── pangenome_matrix_t0__softcore_list.txt ├── pangenome_matrix_t0_heatmap.pdf ├── pangenome_matrix_t0_heatmap.svg ├── unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algCOG_Pfam_e0_.venn_t0.txt ├── unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algCOG_e0_.venn_t0.txt ├── unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algOMCL_Pfam_e0_.venn_t0.txt ├── unique_UnculturedbacteriumplasmidpRSB203_f0_0taxa_algOMCL_e0_.venn_t0.txt └── venn_t0.pdf ├── sample_plasmids_gbk ├── A.txt ├── B.txt ├── E_coli_ST131_plasmid_pKC394.gb ├── E_coli_plasmid_pMUR050.gb ├── IncN_plasmid_R46.gb ├── K_oxytoca_plasmid_pKOX105.gb ├── K_pneumoniae_12_plasmid_12.gb ├── K_pneumoniae_9_plasmid_9.gb ├── K_pneumoniae_KP96_plasmid_pKP96.gb ├── S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb ├── Uncultured_bacterium_plasmid_pRSB201.gb ├── Uncultured_bacterium_plasmid_pRSB203.gb ├── Uncultured_bacterium_plasmid_pRSB205.gb ├── Uncultured_bacterium_plasmid_pRSB206.gb └── include_list.txt ├── sample_plasmids_gbk_homologues ├── E_coli_ST131_plasmid_pKC394.gb.faa ├── E_coli_ST131_plasmid_pKC394.gb.fasta ├── E_coli_ST131_plasmid_pKC394.gb.fasta.phr ├── E_coli_ST131_plasmid_pKC394.gb.fasta.pin ├── E_coli_ST131_plasmid_pKC394.gb.fasta.psq ├── E_coli_ST131_plasmid_pKC394.gb.fna ├── E_coli_plasmid_pMUR050.gb.faa ├── E_coli_plasmid_pMUR050.gb.fasta ├── E_coli_plasmid_pMUR050.gb.fasta.phr ├── E_coli_plasmid_pMUR050.gb.fasta.pin ├── E_coli_plasmid_pMUR050.gb.fasta.psq ├── E_coli_plasmid_pMUR050.gb.fna ├── IncN_plasmid_R46.gb.faa ├── IncN_plasmid_R46.gb.fasta ├── IncN_plasmid_R46.gb.fasta.phr ├── IncN_plasmid_R46.gb.fasta.pin ├── IncN_plasmid_R46.gb.fasta.psq ├── IncN_plasmid_R46.gb.fna ├── K_oxytoca_plasmid_pKOX105.gb.faa ├── K_oxytoca_plasmid_pKOX105.gb.fasta ├── K_oxytoca_plasmid_pKOX105.gb.fasta.phr ├── K_oxytoca_plasmid_pKOX105.gb.fasta.pin ├── K_oxytoca_plasmid_pKOX105.gb.fasta.psq ├── K_oxytoca_plasmid_pKOX105.gb.fna ├── K_pneumoniae_12_plasmid_12.gb.faa ├── K_pneumoniae_12_plasmid_12.gb.fasta ├── K_pneumoniae_12_plasmid_12.gb.fasta.phr ├── K_pneumoniae_12_plasmid_12.gb.fasta.pin ├── K_pneumoniae_12_plasmid_12.gb.fasta.psq ├── K_pneumoniae_12_plasmid_12.gb.fna ├── K_pneumoniae_9_plasmid_9.gb.faa ├── K_pneumoniae_9_plasmid_9.gb.fasta ├── K_pneumoniae_9_plasmid_9.gb.fasta.phr ├── K_pneumoniae_9_plasmid_9.gb.fasta.pin ├── K_pneumoniae_9_plasmid_9.gb.fasta.psq ├── K_pneumoniae_9_plasmid_9.gb.fna ├── K_pneumoniae_KP96_plasmid_pKP96.gb.faa ├── K_pneumoniae_KP96_plasmid_pKP96.gb.fasta ├── K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.phr ├── K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.pin ├── K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.psq ├── K_pneumoniae_KP96_plasmid_pKP96.gb.fna ├── S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.faa ├── S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta ├── S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.phr ├── S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.pin ├── S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.psq ├── S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fna ├── Uncultured_bacterium_plasmid_pRSB201.gb.faa ├── Uncultured_bacterium_plasmid_pRSB201.gb.fasta ├── Uncultured_bacterium_plasmid_pRSB201.gb.fasta.phr ├── Uncultured_bacterium_plasmid_pRSB201.gb.fasta.pin ├── Uncultured_bacterium_plasmid_pRSB201.gb.fasta.psq ├── Uncultured_bacterium_plasmid_pRSB201.gb.fna ├── Uncultured_bacterium_plasmid_pRSB203.gb.faa ├── Uncultured_bacterium_plasmid_pRSB203.gb.fasta ├── Uncultured_bacterium_plasmid_pRSB203.gb.fasta.phr ├── Uncultured_bacterium_plasmid_pRSB203.gb.fasta.pin ├── Uncultured_bacterium_plasmid_pRSB203.gb.fasta.psq ├── Uncultured_bacterium_plasmid_pRSB203.gb.fna ├── Uncultured_bacterium_plasmid_pRSB205.gb.faa ├── Uncultured_bacterium_plasmid_pRSB205.gb.fasta ├── Uncultured_bacterium_plasmid_pRSB205.gb.fasta.phr ├── Uncultured_bacterium_plasmid_pRSB205.gb.fasta.pin ├── Uncultured_bacterium_plasmid_pRSB205.gb.fasta.psq ├── Uncultured_bacterium_plasmid_pRSB205.gb.fna ├── Uncultured_bacterium_plasmid_pRSB206.gb.faa ├── Uncultured_bacterium_plasmid_pRSB206.gb.fasta ├── Uncultured_bacterium_plasmid_pRSB206.gb.fasta.phr ├── Uncultured_bacterium_plasmid_pRSB206.gb.fasta.pin ├── Uncultured_bacterium_plasmid_pRSB206.gb.fasta.psq ├── Uncultured_bacterium_plasmid_pRSB206.gb.fna ├── UnculturedbacteriumplasmidpRSB203_f0_alltaxa_algBDBH_e0_.cluster_list ├── UnculturedbacteriumplasmidpRSB203_f0_alltaxa_algBDBH_e0_ │ ├── 601_repA.faa │ ├── 601_repA.fna │ ├── 602_resP.faa │ ├── 602_resP.fna │ ├── 614_hypothetical_protein.faa │ ├── 614_hypothetical_protein.fna │ ├── 615_korB.faa │ ├── 615_korB.fna │ ├── 617_korA.faa │ ├── 617_korA.fna │ ├── 618_traM.faa │ ├── 618_traM.fna │ ├── 621_traC.faa │ ├── 621_traC.fna │ ├── 622_eex.faa │ ├── 622_eex.fna │ ├── 623_traD.faa │ ├── 623_traD.fna │ ├── 625_traE.faa │ ├── 625_traE.fna │ ├── 626_traO.faa │ ├── 626_traO.fna │ ├── 627_traF.faa │ ├── 627_traF.fna │ ├── 628_traG.faa │ ├── 628_traG.fna │ ├── 629_nuc.faa │ ├── 629_nuc.fna │ ├── 631_traI.faa │ ├── 631_traI.fna │ ├── 632_traJ.faa │ ├── 632_traJ.fna │ ├── 634_stbA.faa │ ├── 634_stbA.fna │ ├── 635_stbB.faa │ ├── 635_stbB.fna │ ├── 636_stbC.faa │ ├── 636_stbC.fna │ ├── 639_ccgAI.faa │ ├── 639_ccgAI.fna │ ├── 646_mucA.faa │ ├── 646_mucA.fna │ ├── 647_mucB.faa │ ├── 647_mucB.fna │ ├── 648_mpr.faa │ ├── 648_mpr.fna │ ├── 649_ardK.faa │ └── 649_ardK.fna ├── UnculturedbacteriumplasmidpRSB203_f0_alltaxa_algCOG_e0_.cluster_list ├── UnculturedbacteriumplasmidpRSB203_f0_alltaxa_algCOG_e0_ │ ├── 601_repA.faa │ ├── 601_repA.fna │ ├── 602_resP.faa │ ├── 602_resP.fna │ ├── 614_hypothetical_protein.faa │ ├── 614_hypothetical_protein.fna │ ├── 615_korB.faa │ ├── 615_korB.fna │ ├── 617_korA.faa │ ├── 617_korA.fna │ ├── 618_traM.faa │ ├── 618_traM.fna │ ├── 621_traC.faa │ ├── 621_traC.fna │ ├── 622_eex.faa │ ├── 622_eex.fna │ ├── 623_traD.faa │ ├── 623_traD.fna │ ├── 625_traE.faa │ ├── 625_traE.fna │ ├── 626_traO.faa │ ├── 626_traO.fna │ ├── 627_traF.faa │ ├── 627_traF.fna │ ├── 628_traG.faa │ ├── 628_traG.fna │ ├── 629_nuc.faa │ ├── 629_nuc.fna │ ├── 631_traI.faa │ ├── 631_traI.fna │ ├── 632_traJ.faa │ ├── 632_traJ.fna │ ├── 634_stbA.faa │ ├── 634_stbA.fna │ ├── 635_stbB.faa │ ├── 635_stbB.fna │ ├── 636_stbC.faa │ ├── 636_stbC.fna │ ├── 639_ccgAI.faa │ ├── 639_ccgAI.fna │ ├── 646_mucA.faa │ ├── 646_mucA.fna │ ├── 647_mucB.faa │ ├── 647_mucB.fna │ ├── 648_mpr.faa │ ├── 648_mpr.fna │ ├── 649_ardK.faa │ └── 649_ardK.fna ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _E_coli_ST131_plasmid_pKC394.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _E_coli_plasmid_pMUR050.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _IncN_plasmid_R46.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _K_oxytoca_plasmid_pKOX105.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _K_pneumoniae_12_plasmid_12.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _K_pneumoniae_9_plasmid_9.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _K_pneumoniae_KP96_plasmid_pKP96.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB201.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB203.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB205.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_E_coli_ST131_plasmid_pKC394.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_E_coli_plasmid_pMUR050.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_IncN_plasmid_R46.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_oxytoca_plasmid_pKOX105.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_12_plasmid_12.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_9_plasmid_9.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_K_pneumoniae_KP96_plasmid_pKP96.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_S_enterica_subsp_enterica_serovar_Dublin_plasmid_pMAK2.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_Uncultured_bacterium_plasmid_pRSB201.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_Uncultured_bacterium_plasmid_pRSB203.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_Uncultured_bacterium_plasmid_pRSB205.gb.fasta.blast.gz ├── _Uncultured_bacterium_plasmid_pRSB206.gb.fasta_Uncultured_bacterium_plasmid_pRSB206.gb.fasta.blast.gz ├── diamond.txt ├── dryrun.txt └── input_order.txt ├── sample_transcripts.fna ├── sample_transcripts_fasta ├── Esterel.trinity.fna.bz2 ├── Franka.trinity.fna.bz2 ├── Hs_Turkey-19-24.trinity.fna.bz2 ├── README.txt └── flcdnas_Hnijo.fna.gz ├── test_Streptococcus ├── A.list ├── B.list └── test_Streptococcus_download_list.txt ├── test_barley ├── cds │ ├── HOWTO.txt │ ├── SBCC073.list │ ├── Scarlett.list │ ├── leaf.list │ ├── ref.list │ └── spontaneum.list ├── seqs │ ├── cds.sh │ ├── cdsCPP.sh │ └── wgetlist.txt └── suppl_scripts │ ├── SOURCE.txt │ ├── _add_Pfam_domains.pl │ └── _plot_heatmap.R ├── test_get_homologues.t ├── transcripts2cds.pl ├── transcripts2cdsCPP.pl └── user_utils ├── dNdS ├── README.md ├── align.tbz ├── calc_kaks.pl ├── example.png ├── kaks.tab ├── kaks4R.tab ├── kaks_vs_occupancy_stats.R └── my_99726_TR31812-c1_g1_i1_aln.fna ├── ensembl ├── PlantCompUtils.pm ├── README.md ├── downloads │ └── README.txt ├── ens_pangene_analysis.pl └── pics │ ├── POCP.matrix_heatmap.svg │ ├── core_gene.tab_core_both.png │ ├── pan_gene.tab_pan.png │ ├── pan_gene_nosingles.tab_pan.png │ └── pangenome_matrix__shell.png ├── get_homologues_to_pathway-tools ├── README.md ├── compile_pangenome_output.py └── reconstruct_gbk_from_get_homologues_output.py ├── normalize ├── README.md ├── images │ ├── effect_nucl_cov.png │ ├── effect_prot_id.png │ ├── singleton_len_nucl.png │ └── singleton_len_prot.png ├── norm_bitscore.pl ├── sample.blastp.gz └── sample.blastp.norm └── polyploid_trees ├── README.md └── _trim_MSA_block.pl /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/.gitignore -------------------------------------------------------------------------------- /CHANGES.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/CHANGES.txt -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /HOWTOTettelin.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/HOWTOTettelin.txt -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/README.md -------------------------------------------------------------------------------- /README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/README.txt -------------------------------------------------------------------------------- /TODO.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/TODO.txt -------------------------------------------------------------------------------- /_cluster_makeHomolog.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/_cluster_makeHomolog.pl -------------------------------------------------------------------------------- /_cluster_makeInparalog.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/_cluster_makeInparalog.pl -------------------------------------------------------------------------------- /_cluster_makeIsoform.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/_cluster_makeIsoform.pl -------------------------------------------------------------------------------- /_cluster_makeOrtholog.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/_cluster_makeOrtholog.pl -------------------------------------------------------------------------------- /_split_blast.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/_split_blast.pl -------------------------------------------------------------------------------- /_split_hmmscan.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/_split_hmmscan.pl -------------------------------------------------------------------------------- /add_pancore_matrices.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/add_pancore_matrices.pl -------------------------------------------------------------------------------- /add_pangenome_matrices.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/add_pangenome_matrices.pl -------------------------------------------------------------------------------- /annotate_cluster.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/annotate_cluster.pl -------------------------------------------------------------------------------- /bin/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/bin/README.txt -------------------------------------------------------------------------------- /check_BDBHs.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/check_BDBHs.pl -------------------------------------------------------------------------------- /compare_clusters.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/compare_clusters.pl -------------------------------------------------------------------------------- /cpanfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/cpanfile -------------------------------------------------------------------------------- /db/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/db/README.txt -------------------------------------------------------------------------------- /docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/docker/Dockerfile -------------------------------------------------------------------------------- /download_genomes_ncbi.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/download_genomes_ncbi.pl -------------------------------------------------------------------------------- /get_homologues-est.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/get_homologues-est.pl -------------------------------------------------------------------------------- /get_homologues.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/get_homologues.pl -------------------------------------------------------------------------------- /hcluster_pangenome_matrix.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/hcluster_pangenome_matrix.sh -------------------------------------------------------------------------------- /install.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/install.pl -------------------------------------------------------------------------------- /lib/ForkManager.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/ForkManager.pm -------------------------------------------------------------------------------- /lib/HPCluster.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/HPCluster.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/AUTHORS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/AUTHORS -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/AnnotatableI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/AnnotatableI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Annotation/Collection.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Annotation/Collection.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Annotation/Comment.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Annotation/Comment.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Annotation/DBLink.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Annotation/DBLink.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Annotation/OntologyTerm.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Annotation/OntologyTerm.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Annotation/Reference.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Annotation/Reference.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Annotation/SimpleValue.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Annotation/SimpleValue.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Annotation/Target.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Annotation/Target.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Annotation/TypeManager.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Annotation/TypeManager.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/AnnotationCollectionI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/AnnotationCollectionI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/AnnotationI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/AnnotationI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/Chain.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/Chain.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/Collection.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/Collection.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/GeneMapper.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/GeneMapper.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/Graph.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/Graph.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/MapperI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/MapperI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/Pair.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/Pair.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/Result.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/Result.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/Result/Gap.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/Result/Gap.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/Result/Match.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/Result/Match.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/ResultI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/ResultI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Coordinate/Utils.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Coordinate/Utils.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/DB/Taxonomy.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/DB/Taxonomy.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/DB/Taxonomy/entrez.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/DB/Taxonomy/entrez.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/DB/Taxonomy/flatfile.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/DB/Taxonomy/flatfile.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/DB/Taxonomy/list.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/DB/Taxonomy/list.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/DB/WebDBSeqI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/DB/WebDBSeqI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/DescribableI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/DescribableI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Factory/AnalysisI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Factory/AnalysisI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Factory/DriverFactory.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Factory/DriverFactory.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Factory/HitFactoryI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Factory/HitFactoryI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Factory/MapFactoryI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Factory/MapFactoryI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Factory/ObjectFactory.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Factory/ObjectFactory.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Factory/TreeFactoryI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Factory/TreeFactoryI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/FeatureHolderI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/FeatureHolderI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graph/Edge.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graph/Edge.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graph/IO.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graph/IO.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graph/IO/dip.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graph/IO/dip.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graph/IO/psi_xml.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graph/IO/psi_xml.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graph/ProteinGraph.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graph/ProteinGraph.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graph/SimpleGraph.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graph/SimpleGraph.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Feature.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Feature.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/FeatureBase.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/FeatureBase.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/FeatureFile.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/FeatureFile.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/arrow.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/arrow.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/box.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/box.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/cds.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/cds.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/dna.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/dna.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/dot.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/dot.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/ex.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/ex.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/flag.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/flag.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/gene.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/gene.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/group.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/group.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/image.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/image.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/line.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/line.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/minmax.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/minmax.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/oval.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/oval.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/span.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/span.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/track.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/track.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/wave.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/wave.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/xyplot.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Glyph/xyplot.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Panel.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Panel.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Pictogram.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Pictogram.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/RendererI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/RendererI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Graphics/Util.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Graphics/Util.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/IdentifiableI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/IdentifiableI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/LocatableSeq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/LocatableSeq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Location/Atomic.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Location/Atomic.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Location/Fuzzy.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Location/Fuzzy.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Location/Simple.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Location/Simple.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Location/Split.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Location/Split.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/LocationI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/LocationI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Perl.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Perl.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/PrimarySeq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/PrimarySeq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/PrimarySeqI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/PrimarySeqI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/README: -------------------------------------------------------------------------------- 1 | Removed all modules not required by get_homologues.pl 2 | Jan 2011 3 | -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Range.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Range.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/RangeI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/RangeI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Root/Exception.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Root/Exception.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Root/HTTPget.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Root/HTTPget.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Root/IO.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Root/IO.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Root/Root.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Root/Root.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Root/RootI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Root/RootI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Root/Storable.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Root/Storable.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Root/Version.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Root/Version.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/BaseSeqProcessor.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/BaseSeqProcessor.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/EncodedSeq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/EncodedSeq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/LargeLocatableSeq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/LargeLocatableSeq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/LargePrimarySeq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/LargePrimarySeq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/LargeSeq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/LargeSeq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/LargeSeqI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/LargeSeqI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/Meta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/Meta.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/Meta/Array.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/Meta/Array.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/MetaI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/MetaI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/PrimaryQual.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/PrimaryQual.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/PrimedSeq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/PrimedSeq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/QualI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/QualI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/Quality.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/Quality.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/RichSeq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/RichSeq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/RichSeqI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/RichSeqI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/SeqBuilder.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/SeqBuilder.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/SeqFactory.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/SeqFactory.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/SeqWithQuality.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/SeqWithQuality.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/SequenceTrace.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/SequenceTrace.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Seq/TraceI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Seq/TraceI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqAnalysisParserI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqAnalysisParserI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeature/Annotated.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeature/Annotated.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeature/Collection.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeature/Collection.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeature/Gene/Exon.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeature/Gene/Exon.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeature/Gene/ExonI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeature/Gene/ExonI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeature/Gene/UTR.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeature/Gene/UTR.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeature/Generic.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeature/Generic.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeature/Primer.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeature/Primer.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeature/SiRNA/Pair.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeature/SiRNA/Pair.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeature/Similarity.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeature/Similarity.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqFeatureI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqFeatureI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/FTHelper.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/FTHelper.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/MultiFile.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/MultiFile.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/abi.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/abi.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/ace.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/ace.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/agave.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/agave.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/alf.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/alf.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/asciitree.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/asciitree.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/bsml.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/bsml.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/bsml_sax.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/bsml_sax.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/chadoxml.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/chadoxml.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/chaos.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/chaos.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/chaosxml.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/chaosxml.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/ctf.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/ctf.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/embl.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/embl.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/entrezgene.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/entrezgene.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/excel.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/excel.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/exp.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/exp.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/fasta.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/fastq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/fastq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/game.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/game.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/game/gameSubs.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/game/gameSubs.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/game/gameWriter.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/game/gameWriter.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/game/seqHandler.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/game/seqHandler.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/gcg.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/gcg.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/genbank.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/genbank.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/interpro.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/interpro.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/kegg.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/kegg.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/largefasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/largefasta.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/lasergene.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/lasergene.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/locuslink.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/locuslink.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/metafasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/metafasta.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/phd.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/phd.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/pir.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/pir.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/pln.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/pln.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/qual.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/qual.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/raw.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/raw.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/scf.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/scf.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/strider.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/strider.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/swiss.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/swiss.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/tab.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/tab.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/table.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/table.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/tigr.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/tigr.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/tigrxml.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/tigrxml.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/tinyseq.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/tinyseq.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqIO/ztr.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqIO/ztr.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/SeqUtils.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/SeqUtils.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Species.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Species.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Taxon.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Taxon.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tools/CodonTable.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tools/CodonTable.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tools/GFF.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tools/GFF.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tools/GuessSeqFormat.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tools/GuessSeqFormat.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tools/IUPAC.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tools/IUPAC.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/AlleleNode.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/AlleleNode.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/Compatible.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/Compatible.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/DistanceFactory.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/DistanceFactory.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/Draw/Cladogram.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/Draw/Cladogram.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/Node.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/Node.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/NodeI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/NodeI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/NodeNHX.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/NodeNHX.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/RandomFactory.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/RandomFactory.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/Statistics.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/Statistics.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/Tree.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/Tree.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/TreeFunctionsI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/TreeFunctionsI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/Bio/Tree/TreeI.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/Bio/Tree/TreeI.pm -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/LICENSE -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/README -------------------------------------------------------------------------------- /lib/bioperl-1.5.2_102/README2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/bioperl-1.5.2_102/README2 -------------------------------------------------------------------------------- /lib/est/TransDecoder_r20140704/LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/est/TransDecoder_r20140704/LICENSE.txt -------------------------------------------------------------------------------- /lib/est/TransDecoder_r20140704/PerlLib/Gene_obj.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/est/TransDecoder_r20140704/PerlLib/Gene_obj.pm -------------------------------------------------------------------------------- /lib/est/TransDecoder_r20140704/PerlLib/TiedHash.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/est/TransDecoder_r20140704/PerlLib/TiedHash.pm -------------------------------------------------------------------------------- /lib/est/TransDecoder_r20140704/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/est/TransDecoder_r20140704/README -------------------------------------------------------------------------------- /lib/est/TransDecoder_r20140704/TransDecoder: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/est/TransDecoder_r20140704/TransDecoder -------------------------------------------------------------------------------- /lib/est/cppcode.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/est/cppcode.pm -------------------------------------------------------------------------------- /lib/est/transcripts.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/est/transcripts.pm -------------------------------------------------------------------------------- /lib/marfil_homology.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/marfil_homology.pm -------------------------------------------------------------------------------- /lib/mview/CHANGES: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/CHANGES -------------------------------------------------------------------------------- /lib/mview/LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/LICENSE.md -------------------------------------------------------------------------------- /lib/mview/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/Makefile -------------------------------------------------------------------------------- /lib/mview/Makefile.PL: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/Makefile.PL -------------------------------------------------------------------------------- /lib/mview/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/README.md -------------------------------------------------------------------------------- /lib/mview/bin/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/bin/Makefile -------------------------------------------------------------------------------- /lib/mview/bin/mview: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/bin/mview -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/Makefile -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/.buildinfo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/.buildinfo -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/.nojekyll: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/_sources/index.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/_sources/index.txt -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/_static/MView.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/_static/MView.css -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/_static/basic.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/_static/basic.css -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/_static/down.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/_static/down.png -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/_static/file.png -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/_static/jquery.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/_static/jquery.js -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/_static/minus.png -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/_static/plus.png -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/_static/up.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/_static/up.png -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/contents.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/contents.html -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/etc/Licence.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/etc/Licence.html -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/genindex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/genindex.html -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/index.html -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/manual/faq.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/manual/faq.html -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/manual/intro.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/manual/intro.html -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/manual/manual.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/manual/manual.html -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/objects.inv -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/search.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/search.html -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/build/html/searchindex.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/build/html/searchindex.js -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/_static/MView.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/_static/MView.css -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/conf.py -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/contents.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/contents.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/etc/Licence.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/etc/Licence.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/index.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/install/perl.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/install/perl.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/install/unix.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/install/unix.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/install/windows.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/install/windows.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/manual/blast/rules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/manual/blast/rules.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/manual/faq.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/manual/faq.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/manual/formats_in.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/manual/formats_in.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/manual/formats_out.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/manual/formats_out.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/manual/intro.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/manual/intro.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/manual/manual.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/manual/manual.rst -------------------------------------------------------------------------------- /lib/mview/doc/Sphinx/source/manual/unused.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/Sphinx/source/manual/unused.txt -------------------------------------------------------------------------------- /lib/mview/doc/data/MAKE_FIGURES: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/MAKE_FIGURES -------------------------------------------------------------------------------- /lib/mview/doc/data/blastn.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/blastn.dat -------------------------------------------------------------------------------- /lib/mview/doc/data/clustal.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/clustal.dat -------------------------------------------------------------------------------- /lib/mview/doc/data/commented.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/commented.dat -------------------------------------------------------------------------------- /lib/mview/doc/data/data.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/data.dat -------------------------------------------------------------------------------- /lib/mview/doc/data/data_ncbi_id.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/data_ncbi_id.dat -------------------------------------------------------------------------------- /lib/mview/doc/data/data_srs.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/data_srs.dat -------------------------------------------------------------------------------- /lib/mview/doc/data/data_sw_id.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/data_sw_id.dat -------------------------------------------------------------------------------- /lib/mview/doc/data/dssp.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/dssp.dat -------------------------------------------------------------------------------- /lib/mview/doc/data/listcolors: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/listcolors -------------------------------------------------------------------------------- /lib/mview/doc/data/listcss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/listcss -------------------------------------------------------------------------------- /lib/mview/doc/data/listgroups: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/doc/data/listgroups -------------------------------------------------------------------------------- /lib/mview/doc/html: -------------------------------------------------------------------------------- 1 | Sphinx/build/html -------------------------------------------------------------------------------- /lib/mview/etc/COPYRIGHT.templ: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/etc/COPYRIGHT.templ -------------------------------------------------------------------------------- /lib/mview/etc/MAKEFILE.templ: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/etc/MAKEFILE.templ -------------------------------------------------------------------------------- /lib/mview/etc/Makefile.example: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/etc/Makefile.example -------------------------------------------------------------------------------- /lib/mview/install.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/install.pl -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/Alignment.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/Alignment.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/ColorMixin.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/ColorMixin.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/Consensus.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/Consensus.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/Conservation.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/Conservation.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/Header.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/Header.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/Row.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/Row.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/Ruler.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/Ruler.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/Sequence.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/Sequence.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Align/Special.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Align/Special.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Align.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Align.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Base.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Base.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/BLAST.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/BLAST.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/BLAST0.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/BLAST0.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/BLAST1.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/BLAST1.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/BLAST2.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/BLAST2.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/CLUSTAL.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/CLUSTAL.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/FASTA.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/FASTA.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/FASTA1.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/FASTA1.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/FASTA2.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/FASTA2.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/FASTA3.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/FASTA3.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/FASTA3X.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/FASTA3X.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/HSSP.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/HSSP.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/JNETZ.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/JNETZ.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/MAF.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/MAF.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/MIPS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/MIPS.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/MSF.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/MSF.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/MULTAS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/MULTAS.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/PIR.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/PIR.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/Pearson.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/Pearson.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Format/Plain.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Format/Plain.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Row.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Row.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/RowInfoMixin.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/RowInfoMixin.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Scheduler.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Scheduler.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Build/Search.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Build/Search.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Color/ColorMap.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Color/ColorMap.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Color/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Color/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Color/Palette.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Color/Palette.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Convert.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Convert.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Any.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Any.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Display.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Display.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Header.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Header.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Out/HTML.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Out/HTML.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Out/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Out/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Out/Text.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Out/Text.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Panel.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Panel.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Ruler.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Ruler.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Sequence.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Sequence.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Display/Track.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Display/Track.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/GroupMap.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/GroupMap.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Manager.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Manager.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Option/Arguments.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Option/Arguments.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Option/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Option/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Option/Options.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Option/Options.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Option/Parameters.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Option/Parameters.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Option/Parser.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Option/Parser.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Option/Types.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Option/Types.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/SRS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/SRS.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Sequence.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Sequence.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Sequence/Base.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Sequence/Base.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Sequence/Forward.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Sequence/Forward.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Sequence/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Sequence/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/MView/Sequence/Reverse.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/MView/Sequence/Reverse.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Block.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Block.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/BlockKeeper.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/BlockKeeper.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST1.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST1.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST1/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST1/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST1/blastn.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST1/blastn.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST1/blastp.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST1/blastp.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST1/blastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST1/blastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST1/tblastn.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST1/tblastn.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST1/tblastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST1/tblastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST2.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST2.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST2/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST2/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST2/blastn.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST2/blastn.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST2/blastp.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST2/blastp.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST2/blastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST2/blastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST2/tblastn.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST2/tblastn.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST2/tblastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST2/tblastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST2_OF7.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST2_OF7.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/BLAST2_OF7/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/BLAST2_OF7/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/CLUSTAL.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/CLUSTAL.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA1.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA1.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA1/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA1/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA1/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA1/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2/align.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2/align.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2/lalign.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2/lalign.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2/ssearch.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2/ssearch.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2/tfasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2/tfasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2_GCG.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2_GCG.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2_GCG/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2_GCG/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA2_GCG/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA2_GCG/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3/fastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3/fastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3/tfasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3/tfasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X/fastm.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X/fastm.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X/fastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X/fastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X/ggsearch.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X/ggsearch.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X/glsearch.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X/glsearch.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X/ssearch.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X/ssearch.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X/tfasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X/tfasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/FASTA3X/tfastm.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/FASTA3X/tfastm.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/HSSP.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/HSSP.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/JNETZ.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/JNETZ.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/MAF.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/MAF.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/MIPS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/MIPS.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/MSF.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/MSF.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/MULTAS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/MULTAS.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/PIR.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/PIR.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/Pearson.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/Pearson.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Format/Plain.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Format/Plain.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/ReadFile.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/ReadFile.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/ReadText.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/ReadText.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Record.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Record.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Scanner.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Scanner.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Stream.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Stream.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Parse/Strings.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Parse/Strings.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/SRS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/SRS.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Util/File.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Util/File.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Util/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Util/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Util/Math.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Util/Math.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Util/Object.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Util/Object.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Util/Regexp.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Util/Regexp.pm -------------------------------------------------------------------------------- /lib/mview/lib/Bio/Util/System.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Bio/Util/System.pm -------------------------------------------------------------------------------- /lib/mview/lib/Getopt.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Getopt.pm -------------------------------------------------------------------------------- /lib/mview/lib/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST1.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST1.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST1/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST1/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST1/blastn.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST1/blastn.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST1/blastp.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST1/blastp.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST1/blastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST1/blastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST1/tblastn.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST1/tblastn.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST1/tblastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST1/tblastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST2.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST2.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST2/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST2/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST2/blastn.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST2/blastn.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST2/blastp.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST2/blastp.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST2/blastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST2/blastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST2/tblastn.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST2/tblastn.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST2/tblastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST2/tblastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST2_OF7.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST2_OF7.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLAST2_OF7/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLAST2_OF7/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/BLOCKS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/BLOCKS.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/CLUSTAL.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/CLUSTAL.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA1.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA1.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA1/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA1/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA1/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA1/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA2.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA2.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA2/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA2/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA2/align.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA2/align.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA2/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA2/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA2/lalign.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA2/lalign.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA2/ssearch.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA2/ssearch.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA2/tfasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA2/tfasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3/fastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3/fastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3/tfasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3/tfasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X/fastm.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X/fastm.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X/fastx.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X/fastx.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X/ggsearch.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X/ggsearch.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X/glsearch.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X/glsearch.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X/ssearch.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X/ssearch.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X/tfasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X/tfasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/FASTA3X/tfastm.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/FASTA3X/tfastm.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/GCG_FASTA2.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/GCG_FASTA2.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/GCG_FASTA2/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/GCG_FASTA2/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/GCG_FASTA2/fasta.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/GCG_FASTA2/fasta.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/HSSP.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/HSSP.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/JNETZ.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/JNETZ.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/MAF.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/MAF.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/MIPS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/MIPS.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/MSF.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/MSF.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/MULTAS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/MULTAS.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/PIR.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/PIR.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/Pearson.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/Pearson.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/Plain.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/Plain.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/Slurp.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/Slurp.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/attic/EMBL.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/attic/EMBL.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/attic/FT.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/attic/FT.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/attic/Genbank.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/attic/Genbank.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Format/attic/SIM.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Format/attic/SIM.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Makefile -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Math.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Math.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Message.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Message.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Record.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Record.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Regexps.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Regexps.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Stream.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Stream.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/Substring.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/Substring.pm -------------------------------------------------------------------------------- /lib/mview/lib/NPB/Parse/attic/Index.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/NPB/Parse/attic/Index.pm -------------------------------------------------------------------------------- /lib/mview/lib/Universal.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/lib/Universal.pm -------------------------------------------------------------------------------- /lib/mview/t/test_Bio::MView::Sequence.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/mview/t/test_Bio::MView::Sequence.pl -------------------------------------------------------------------------------- /lib/phyTools.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/lib/phyTools.pm -------------------------------------------------------------------------------- /make_nr_pangenome_matrix.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/make_nr_pangenome_matrix.pl -------------------------------------------------------------------------------- /manual_get_homologues-est.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/manual_get_homologues-est.pdf -------------------------------------------------------------------------------- /manual_get_homologues.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/manual_get_homologues.pdf -------------------------------------------------------------------------------- /pangenome_tutorial.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/pangenome_tutorial.html -------------------------------------------------------------------------------- /parse_pangenome_matrix.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/parse_pangenome_matrix.pl -------------------------------------------------------------------------------- /pfam_enrich.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/pfam_enrich.pl -------------------------------------------------------------------------------- /pics/EST.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/pics/EST.jpg -------------------------------------------------------------------------------- /pics/logoARAID.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/pics/logoARAID.gif -------------------------------------------------------------------------------- /pics/logoCSIC.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/pics/logoCSIC.png -------------------------------------------------------------------------------- /pics/logoELIXIRES.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/pics/logoELIXIRES.png -------------------------------------------------------------------------------- /pics/logoUNAM.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/pics/logoUNAM.png -------------------------------------------------------------------------------- /pics/summary.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/pics/summary.jpg -------------------------------------------------------------------------------- /plot_matrix_heatmap.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/plot_matrix_heatmap.sh -------------------------------------------------------------------------------- /plot_pancore_matrix.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/plot_pancore_matrix.pl -------------------------------------------------------------------------------- /sample.HPC.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample.HPC.conf -------------------------------------------------------------------------------- /sample_buch_fasta/Buch_aph_APS.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_buch_fasta/Buch_aph_APS.faa -------------------------------------------------------------------------------- /sample_buch_fasta/Buch_aph_Bp.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_buch_fasta/Buch_aph_Bp.faa -------------------------------------------------------------------------------- /sample_buch_fasta/Buch_aph_Cc.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_buch_fasta/Buch_aph_Cc.faa -------------------------------------------------------------------------------- /sample_buch_fasta/Buch_aphid_Sg.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_buch_fasta/Buch_aphid_Sg.faa -------------------------------------------------------------------------------- /sample_cluster.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_cluster.fna -------------------------------------------------------------------------------- /sample_intersection/10_mrx.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/10_mrx.faa -------------------------------------------------------------------------------- /sample_intersection/11_blaCTX-M-1.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/11_blaCTX-M-1.faa -------------------------------------------------------------------------------- /sample_intersection/13_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/13_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/159_intI1.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/159_intI1.faa -------------------------------------------------------------------------------- /sample_intersection/160_oxa2.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/160_oxa2.faa -------------------------------------------------------------------------------- /sample_intersection/163_unknown.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/163_unknown.faa -------------------------------------------------------------------------------- /sample_intersection/166_unknown.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/166_unknown.faa -------------------------------------------------------------------------------- /sample_intersection/168_unknown.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/168_unknown.faa -------------------------------------------------------------------------------- /sample_intersection/170_tetA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/170_tetA.faa -------------------------------------------------------------------------------- /sample_intersection/171_unknown.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/171_unknown.faa -------------------------------------------------------------------------------- /sample_intersection/172_unknown.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/172_unknown.faa -------------------------------------------------------------------------------- /sample_intersection/173_arsR.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/173_arsR.faa -------------------------------------------------------------------------------- /sample_intersection/174_arsD.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/174_arsD.faa -------------------------------------------------------------------------------- /sample_intersection/175_arsA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/175_arsA.faa -------------------------------------------------------------------------------- /sample_intersection/176_arsB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/176_arsB.faa -------------------------------------------------------------------------------- /sample_intersection/177_arsC.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/177_arsC.faa -------------------------------------------------------------------------------- /sample_intersection/198_TnpA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/198_TnpA.faa -------------------------------------------------------------------------------- /sample_intersection/200_AacA4.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/200_AacA4.faa -------------------------------------------------------------------------------- /sample_intersection/201_VIM-1.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/201_VIM-1.faa -------------------------------------------------------------------------------- /sample_intersection/225_delta-FipA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/225_delta-FipA.faa -------------------------------------------------------------------------------- /sample_intersection/226_TnpA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/226_TnpA.faa -------------------------------------------------------------------------------- /sample_intersection/228_truncated_TnpA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/228_truncated_TnpA.faa -------------------------------------------------------------------------------- /sample_intersection/229_QnrS1.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/229_QnrS1.faa -------------------------------------------------------------------------------- /sample_intersection/230_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/230_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/231_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/231_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/232_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/232_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/233_YdaA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/233_YdaA.faa -------------------------------------------------------------------------------- /sample_intersection/234_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/234_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/235_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/235_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/236_putative_DeoR-type_t...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/236_putative_DeoR-type_t...faa -------------------------------------------------------------------------------- /sample_intersection/238_TnpA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/238_TnpA.faa -------------------------------------------------------------------------------- /sample_intersection/240_putative_invertase-r...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/240_putative_invertase-r...faa -------------------------------------------------------------------------------- /sample_intersection/241_PilT.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/241_PilT.faa -------------------------------------------------------------------------------- /sample_intersection/242_TnpA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/242_TnpA.faa -------------------------------------------------------------------------------- /sample_intersection/243_TnpM.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/243_TnpM.faa -------------------------------------------------------------------------------- /sample_intersection/245_dfrA14.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/245_dfrA14.faa -------------------------------------------------------------------------------- /sample_intersection/246_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/246_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/250_putative_mobilizatio...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/250_putative_mobilizatio...faa -------------------------------------------------------------------------------- /sample_intersection/253_transposition_modula...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/253_transposition_modula...faa -------------------------------------------------------------------------------- /sample_intersection/255_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/255_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/264_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/264_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/268_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/268_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/279_transposase.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/279_transposase.faa -------------------------------------------------------------------------------- /sample_intersection/280_transposase.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/280_transposase.faa -------------------------------------------------------------------------------- /sample_intersection/281_phage_integrase_fami...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/281_phage_integrase_fami...faa -------------------------------------------------------------------------------- /sample_intersection/282_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/282_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/286_streptomycin_phospho...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/286_streptomycin_phospho...faa -------------------------------------------------------------------------------- /sample_intersection/288_resolvase.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/288_resolvase.faa -------------------------------------------------------------------------------- /sample_intersection/289_beta-lactamase.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/289_beta-lactamase.faa -------------------------------------------------------------------------------- /sample_intersection/293_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/293_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/294_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/294_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/295_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/295_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/296_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/296_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/297_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/297_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/298_conserved_hypothetic...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/298_conserved_hypothetic...faa -------------------------------------------------------------------------------- /sample_intersection/299_site-specific_recomb...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/299_site-specific_recomb...faa -------------------------------------------------------------------------------- /sample_intersection/301_putative_transposase.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/301_putative_transposase.faa -------------------------------------------------------------------------------- /sample_intersection/302_conserved_hypothetic...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/302_conserved_hypothetic...faa -------------------------------------------------------------------------------- /sample_intersection/304_transposase-_IS4_fam...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/304_transposase-_IS4_fam...faa -------------------------------------------------------------------------------- /sample_intersection/305_transposase.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/305_transposase.faa -------------------------------------------------------------------------------- /sample_intersection/307_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/307_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/308_conserved_hypothetic...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/308_conserved_hypothetic...faa -------------------------------------------------------------------------------- /sample_intersection/318_TraB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/318_TraB.faa -------------------------------------------------------------------------------- /sample_intersection/321_arsenical_pump-drivi...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/321_arsenical_pump-drivi...faa -------------------------------------------------------------------------------- /sample_intersection/327_TraB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/327_TraB.faa -------------------------------------------------------------------------------- /sample_intersection/338_InsB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/338_InsB.faa -------------------------------------------------------------------------------- /sample_intersection/341_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/341_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/348_group_II_intron-enco...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/348_group_II_intron-enco...faa -------------------------------------------------------------------------------- /sample_intersection/349_transposase_InsF.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/349_transposase_InsF.faa -------------------------------------------------------------------------------- /sample_intersection/34_methyl-accepting_che...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/34_methyl-accepting_che...faa -------------------------------------------------------------------------------- /sample_intersection/350_transposase.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/350_transposase.faa -------------------------------------------------------------------------------- /sample_intersection/351_putative_transposase...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/351_putative_transposase...faa -------------------------------------------------------------------------------- /sample_intersection/352_resolvase.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/352_resolvase.faa -------------------------------------------------------------------------------- /sample_intersection/353_S-formylglutathione_...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/353_S-formylglutathione_...faa -------------------------------------------------------------------------------- /sample_intersection/354_glyoxalase-bleomycin...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/354_glyoxalase-bleomycin...faa -------------------------------------------------------------------------------- /sample_intersection/355_S--hydroxymethyl-glu...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/355_S--hydroxymethyl-glu...faa -------------------------------------------------------------------------------- /sample_intersection/35_tnpA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/35_tnpA.faa -------------------------------------------------------------------------------- /sample_intersection/362_group_II_intron-enco...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/362_group_II_intron-enco...faa -------------------------------------------------------------------------------- /sample_intersection/363_putative_transposase...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/363_putative_transposase...faa -------------------------------------------------------------------------------- /sample_intersection/364_conserved_hypothetic...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/364_conserved_hypothetic...faa -------------------------------------------------------------------------------- /sample_intersection/365_NADH_dehydrogenase-_...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/365_NADH_dehydrogenase-_...faa -------------------------------------------------------------------------------- /sample_intersection/366_excinuclease_ABC-_A_...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/366_excinuclease_ABC-_A_...faa -------------------------------------------------------------------------------- /sample_intersection/367_ISEc8_transposase.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/367_ISEc8_transposase.faa -------------------------------------------------------------------------------- /sample_intersection/368_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/368_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/36_beta-lactamase_CTX-M...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/36_beta-lactamase_CTX-M...faa -------------------------------------------------------------------------------- /sample_intersection/376_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/376_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/379_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/379_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/380_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/380_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/381_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/381_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/382_conserved_hypothetic...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/382_conserved_hypothetic...faa -------------------------------------------------------------------------------- /sample_intersection/383_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/383_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/384_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/384_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/390_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/390_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/391_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/391_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/396_TraK.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/396_TraK.faa -------------------------------------------------------------------------------- /sample_intersection/400_DNA_polymerase-_beta...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/400_DNA_polymerase-_beta...faa -------------------------------------------------------------------------------- /sample_intersection/401_protein_of_unknown_f...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/401_protein_of_unknown_f...faa -------------------------------------------------------------------------------- /sample_intersection/402_conserved_hypothetic...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/402_conserved_hypothetic...faa -------------------------------------------------------------------------------- /sample_intersection/408_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/408_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/413_TraA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/413_TraA.faa -------------------------------------------------------------------------------- /sample_intersection/416_TraL.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/416_TraL.faa -------------------------------------------------------------------------------- /sample_intersection/417_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/417_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/420_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/420_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/434_qnrA1.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/434_qnrA1.faa -------------------------------------------------------------------------------- /sample_intersection/435_ampR.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/435_ampR.faa -------------------------------------------------------------------------------- /sample_intersection/438_unknown.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/438_unknown.faa -------------------------------------------------------------------------------- /sample_intersection/444_FosA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/444_FosA.faa -------------------------------------------------------------------------------- /sample_intersection/445_tnpA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/445_tnpA.faa -------------------------------------------------------------------------------- /sample_intersection/448_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/448_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/471_putative_relaxase-he...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/471_putative_relaxase-he...faa -------------------------------------------------------------------------------- /sample_intersection/495_MAK2.05.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/495_MAK2.05.faa -------------------------------------------------------------------------------- /sample_intersection/497_ble.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/497_ble.faa -------------------------------------------------------------------------------- /sample_intersection/498_sph.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/498_sph.faa -------------------------------------------------------------------------------- /sample_intersection/501_yahA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/501_yahA.faa -------------------------------------------------------------------------------- /sample_intersection/523_pecM.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/523_pecM.faa -------------------------------------------------------------------------------- /sample_intersection/528_MAK2.40.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/528_MAK2.40.faa -------------------------------------------------------------------------------- /sample_intersection/547_insA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/547_insA.faa -------------------------------------------------------------------------------- /sample_intersection/548_insB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/548_insB.faa -------------------------------------------------------------------------------- /sample_intersection/557_insF.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/557_insF.faa -------------------------------------------------------------------------------- /sample_intersection/601_repA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/601_repA.faa -------------------------------------------------------------------------------- /sample_intersection/602_resP.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/602_resP.faa -------------------------------------------------------------------------------- /sample_intersection/603_ecoRII.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/603_ecoRII.faa -------------------------------------------------------------------------------- /sample_intersection/604_dcm.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/604_dcm.faa -------------------------------------------------------------------------------- /sample_intersection/605_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/605_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/606_type_IV_restriction_...faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/606_type_IV_restriction_...faa -------------------------------------------------------------------------------- /sample_intersection/607_tetC.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/607_tetC.faa -------------------------------------------------------------------------------- /sample_intersection/608_tetB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/608_tetB.faa -------------------------------------------------------------------------------- /sample_intersection/609_tetR.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/609_tetR.faa -------------------------------------------------------------------------------- /sample_intersection/60_ant39.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/60_ant39.faa -------------------------------------------------------------------------------- /sample_intersection/611_strB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/611_strB.faa -------------------------------------------------------------------------------- /sample_intersection/613_kikA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/613_kikA.faa -------------------------------------------------------------------------------- /sample_intersection/614_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/614_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/615_korB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/615_korB.faa -------------------------------------------------------------------------------- /sample_intersection/616_traL.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/616_traL.faa -------------------------------------------------------------------------------- /sample_intersection/617_korA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/617_korA.faa -------------------------------------------------------------------------------- /sample_intersection/618_traM.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/618_traM.faa -------------------------------------------------------------------------------- /sample_intersection/619_traA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/619_traA.faa -------------------------------------------------------------------------------- /sample_intersection/61_linF.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/61_linF.faa -------------------------------------------------------------------------------- /sample_intersection/620_traB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/620_traB.faa -------------------------------------------------------------------------------- /sample_intersection/621_traC.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/621_traC.faa -------------------------------------------------------------------------------- /sample_intersection/622_eex.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/622_eex.faa -------------------------------------------------------------------------------- /sample_intersection/623_traD.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/623_traD.faa -------------------------------------------------------------------------------- /sample_intersection/624_traN.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/624_traN.faa -------------------------------------------------------------------------------- /sample_intersection/625_traE.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/625_traE.faa -------------------------------------------------------------------------------- /sample_intersection/626_traO.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/626_traO.faa -------------------------------------------------------------------------------- /sample_intersection/627_traF.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/627_traF.faa -------------------------------------------------------------------------------- /sample_intersection/628_traG.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/628_traG.faa -------------------------------------------------------------------------------- /sample_intersection/629_nuc.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/629_nuc.faa -------------------------------------------------------------------------------- /sample_intersection/630_fipA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/630_fipA.faa -------------------------------------------------------------------------------- /sample_intersection/631_traI.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/631_traI.faa -------------------------------------------------------------------------------- /sample_intersection/632_traJ.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/632_traJ.faa -------------------------------------------------------------------------------- /sample_intersection/633_traK.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/633_traK.faa -------------------------------------------------------------------------------- /sample_intersection/634_stbA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/634_stbA.faa -------------------------------------------------------------------------------- /sample_intersection/635_stbB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/635_stbB.faa -------------------------------------------------------------------------------- /sample_intersection/636_stbC.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/636_stbC.faa -------------------------------------------------------------------------------- /sample_intersection/637_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/637_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/638_ccgAII.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/638_ccgAII.faa -------------------------------------------------------------------------------- /sample_intersection/639_ccgAI.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/639_ccgAI.faa -------------------------------------------------------------------------------- /sample_intersection/640_ardA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/640_ardA.faa -------------------------------------------------------------------------------- /sample_intersection/641_ccgC.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/641_ccgC.faa -------------------------------------------------------------------------------- /sample_intersection/642_ccgD.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/642_ccgD.faa -------------------------------------------------------------------------------- /sample_intersection/643_ccgEIII.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/643_ccgEIII.faa -------------------------------------------------------------------------------- /sample_intersection/644_ardR.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/644_ardR.faa -------------------------------------------------------------------------------- /sample_intersection/645_ardB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/645_ardB.faa -------------------------------------------------------------------------------- /sample_intersection/646_mucA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/646_mucA.faa -------------------------------------------------------------------------------- /sample_intersection/647_mucB.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/647_mucB.faa -------------------------------------------------------------------------------- /sample_intersection/648_mpr.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/648_mpr.faa -------------------------------------------------------------------------------- /sample_intersection/649_ardK.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/649_ardK.faa -------------------------------------------------------------------------------- /sample_intersection/64_qacEdelta1.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/64_qacEdelta1.faa -------------------------------------------------------------------------------- /sample_intersection/65_sul1.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/65_sul1.faa -------------------------------------------------------------------------------- /sample_intersection/66_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/66_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/68_armA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/68_armA.faa -------------------------------------------------------------------------------- /sample_intersection/69_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/69_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/70_tnpD.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/70_tnpD.faa -------------------------------------------------------------------------------- /sample_intersection/71_mel.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/71_mel.faa -------------------------------------------------------------------------------- /sample_intersection/72_mph1.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/72_mph1.faa -------------------------------------------------------------------------------- /sample_intersection/73_mph2.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/73_mph2.faa -------------------------------------------------------------------------------- /sample_intersection/743_putative_IS91_ORF2.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/743_putative_IS91_ORF2.faa -------------------------------------------------------------------------------- /sample_intersection/744_tnp.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/744_tnp.faa -------------------------------------------------------------------------------- /sample_intersection/74_hypothetical_protein.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/74_hypothetical_protein.faa -------------------------------------------------------------------------------- /sample_intersection/7_transposase_A.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/7_transposase_A.faa -------------------------------------------------------------------------------- /sample_intersection/87_traA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/87_traA.faa -------------------------------------------------------------------------------- /sample_intersection/8_tnpA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/8_tnpA.faa -------------------------------------------------------------------------------- /sample_intersection/9_mphA.faa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/9_mphA.faa -------------------------------------------------------------------------------- /sample_intersection/intersection_t0.cluster_list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/intersection_t0.cluster_list -------------------------------------------------------------------------------- /sample_intersection/pangenome_matrix_genes_t0.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/pangenome_matrix_genes_t0.tab -------------------------------------------------------------------------------- /sample_intersection/pangenome_matrix_t0.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/pangenome_matrix_t0.fasta -------------------------------------------------------------------------------- /sample_intersection/pangenome_matrix_t0.phylip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/pangenome_matrix_t0.phylip -------------------------------------------------------------------------------- /sample_intersection/pangenome_matrix_t0.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/pangenome_matrix_t0.tab -------------------------------------------------------------------------------- /sample_intersection/pangenome_matrix_t0.tabed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/pangenome_matrix_t0.tabed -------------------------------------------------------------------------------- /sample_intersection/pangenome_matrix_t0.tr.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/pangenome_matrix_t0.tr.csv -------------------------------------------------------------------------------- /sample_intersection/pangenome_matrix_t0.tr.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/pangenome_matrix_t0.tr.tab -------------------------------------------------------------------------------- /sample_intersection/pangenome_matrix_t0__shell.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/pangenome_matrix_t0__shell.pdf -------------------------------------------------------------------------------- /sample_intersection/venn_t0.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_intersection/venn_t0.pdf -------------------------------------------------------------------------------- /sample_plasmids_gbk/A.txt: -------------------------------------------------------------------------------- 1 | K_oxytoca_plasmid_pKOX105.gb 2 | -------------------------------------------------------------------------------- /sample_plasmids_gbk/B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_plasmids_gbk/B.txt -------------------------------------------------------------------------------- /sample_plasmids_gbk/E_coli_ST131_plasmid_pKC394.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_plasmids_gbk/E_coli_ST131_plasmid_pKC394.gb -------------------------------------------------------------------------------- /sample_plasmids_gbk/E_coli_plasmid_pMUR050.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_plasmids_gbk/E_coli_plasmid_pMUR050.gb -------------------------------------------------------------------------------- /sample_plasmids_gbk/IncN_plasmid_R46.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_plasmids_gbk/IncN_plasmid_R46.gb -------------------------------------------------------------------------------- /sample_plasmids_gbk/K_oxytoca_plasmid_pKOX105.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_plasmids_gbk/K_oxytoca_plasmid_pKOX105.gb -------------------------------------------------------------------------------- /sample_plasmids_gbk/K_pneumoniae_12_plasmid_12.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_plasmids_gbk/K_pneumoniae_12_plasmid_12.gb -------------------------------------------------------------------------------- /sample_plasmids_gbk/K_pneumoniae_9_plasmid_9.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_plasmids_gbk/K_pneumoniae_9_plasmid_9.gb -------------------------------------------------------------------------------- /sample_plasmids_gbk/include_list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_plasmids_gbk/include_list.txt -------------------------------------------------------------------------------- /sample_plasmids_gbk_homologues/diamond.txt: -------------------------------------------------------------------------------- 1 | diamond job:0 2 | -------------------------------------------------------------------------------- /sample_plasmids_gbk_homologues/dryrun.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /sample_plasmids_gbk_homologues/input_order.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_plasmids_gbk_homologues/input_order.txt -------------------------------------------------------------------------------- /sample_transcripts.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_transcripts.fna -------------------------------------------------------------------------------- /sample_transcripts_fasta/Esterel.trinity.fna.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_transcripts_fasta/Esterel.trinity.fna.bz2 -------------------------------------------------------------------------------- /sample_transcripts_fasta/Franka.trinity.fna.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_transcripts_fasta/Franka.trinity.fna.bz2 -------------------------------------------------------------------------------- /sample_transcripts_fasta/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_transcripts_fasta/README.txt -------------------------------------------------------------------------------- /sample_transcripts_fasta/flcdnas_Hnijo.fna.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/sample_transcripts_fasta/flcdnas_Hnijo.fna.gz -------------------------------------------------------------------------------- /test_Streptococcus/A.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_Streptococcus/A.list -------------------------------------------------------------------------------- /test_Streptococcus/B.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_Streptococcus/B.list -------------------------------------------------------------------------------- /test_barley/cds/HOWTO.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/cds/HOWTO.txt -------------------------------------------------------------------------------- /test_barley/cds/SBCC073.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/cds/SBCC073.list -------------------------------------------------------------------------------- /test_barley/cds/Scarlett.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/cds/Scarlett.list -------------------------------------------------------------------------------- /test_barley/cds/leaf.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/cds/leaf.list -------------------------------------------------------------------------------- /test_barley/cds/ref.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/cds/ref.list -------------------------------------------------------------------------------- /test_barley/cds/spontaneum.list: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/cds/spontaneum.list -------------------------------------------------------------------------------- /test_barley/seqs/cds.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/seqs/cds.sh -------------------------------------------------------------------------------- /test_barley/seqs/cdsCPP.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/seqs/cdsCPP.sh -------------------------------------------------------------------------------- /test_barley/seqs/wgetlist.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/seqs/wgetlist.txt -------------------------------------------------------------------------------- /test_barley/suppl_scripts/SOURCE.txt: -------------------------------------------------------------------------------- 1 | http://floresta.eead.csic.es/plant-pan-genomes/ 2 | -------------------------------------------------------------------------------- /test_barley/suppl_scripts/_add_Pfam_domains.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/suppl_scripts/_add_Pfam_domains.pl -------------------------------------------------------------------------------- /test_barley/suppl_scripts/_plot_heatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_barley/suppl_scripts/_plot_heatmap.R -------------------------------------------------------------------------------- /test_get_homologues.t: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/test_get_homologues.t -------------------------------------------------------------------------------- /transcripts2cds.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/transcripts2cds.pl -------------------------------------------------------------------------------- /transcripts2cdsCPP.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/transcripts2cdsCPP.pl -------------------------------------------------------------------------------- /user_utils/dNdS/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/dNdS/README.md -------------------------------------------------------------------------------- /user_utils/dNdS/align.tbz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/dNdS/align.tbz -------------------------------------------------------------------------------- /user_utils/dNdS/calc_kaks.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/dNdS/calc_kaks.pl -------------------------------------------------------------------------------- /user_utils/dNdS/example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/dNdS/example.png -------------------------------------------------------------------------------- /user_utils/dNdS/kaks.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/dNdS/kaks.tab -------------------------------------------------------------------------------- /user_utils/dNdS/kaks4R.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/dNdS/kaks4R.tab -------------------------------------------------------------------------------- /user_utils/dNdS/kaks_vs_occupancy_stats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/dNdS/kaks_vs_occupancy_stats.R -------------------------------------------------------------------------------- /user_utils/dNdS/my_99726_TR31812-c1_g1_i1_aln.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/dNdS/my_99726_TR31812-c1_g1_i1_aln.fna -------------------------------------------------------------------------------- /user_utils/ensembl/PlantCompUtils.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/ensembl/PlantCompUtils.pm -------------------------------------------------------------------------------- /user_utils/ensembl/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/ensembl/README.md -------------------------------------------------------------------------------- /user_utils/ensembl/downloads/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/ensembl/downloads/README.txt -------------------------------------------------------------------------------- /user_utils/ensembl/ens_pangene_analysis.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/ensembl/ens_pangene_analysis.pl -------------------------------------------------------------------------------- /user_utils/ensembl/pics/POCP.matrix_heatmap.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/ensembl/pics/POCP.matrix_heatmap.svg -------------------------------------------------------------------------------- /user_utils/ensembl/pics/pan_gene.tab_pan.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/ensembl/pics/pan_gene.tab_pan.png -------------------------------------------------------------------------------- /user_utils/normalize/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/normalize/README.md -------------------------------------------------------------------------------- /user_utils/normalize/images/effect_nucl_cov.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/normalize/images/effect_nucl_cov.png -------------------------------------------------------------------------------- /user_utils/normalize/images/effect_prot_id.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/normalize/images/effect_prot_id.png -------------------------------------------------------------------------------- /user_utils/normalize/images/singleton_len_nucl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/normalize/images/singleton_len_nucl.png -------------------------------------------------------------------------------- /user_utils/normalize/images/singleton_len_prot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/normalize/images/singleton_len_prot.png -------------------------------------------------------------------------------- /user_utils/normalize/norm_bitscore.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/normalize/norm_bitscore.pl -------------------------------------------------------------------------------- /user_utils/normalize/sample.blastp.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/normalize/sample.blastp.gz -------------------------------------------------------------------------------- /user_utils/normalize/sample.blastp.norm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/normalize/sample.blastp.norm -------------------------------------------------------------------------------- /user_utils/polyploid_trees/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/polyploid_trees/README.md -------------------------------------------------------------------------------- /user_utils/polyploid_trees/_trim_MSA_block.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eead-csic-compbio/get_homologues/HEAD/user_utils/polyploid_trees/_trim_MSA_block.pl --------------------------------------------------------------------------------