├── 454-tools ├── 454-contigs_not_in_scaffolds.sh ├── 454AlignmentInfo-to-userplot.pl ├── 454PE_to_GAIIPE.pl ├── 454sanger-to-CA.pl ├── ACE_file_format.txt ├── ace-reclaim_contig_ends.pl ├── ace2fasta.pl ├── bb.454contignet ├── chromat-to-454sanger.pl ├── newblermetrics1.0.pl ├── newblermetrics1.2.pl ├── pgm-sff-to-delinked-fasta.pl ├── phantom-454.pl ├── phred-to-454sanger.pl ├── sff-clean.pl └── sff_paired_to_fasta.pl ├── LICENSE ├── README.md ├── blast-tools ├── blast-top_hit.pl ├── blast-view.pl ├── blast2tag.py ├── blast_collate_align.pl └── blatt ├── fqa-tools ├── FastQ.pm ├── FastUtils.pm ├── afa-core.pl ├── afa-join.pl ├── afa-pairwise.pl ├── afa-remove_columns.pl ├── csfa-re-partner.pl ├── fa ├── fa-add_desc.pl ├── fa-add_new_ids.pl ├── fa-analyze_N_runs.pl ├── fa-basepatt_to_gff.pl ├── fa-bridge_scaffold_gaps.pl ├── fa-clean_velvet_contig_names.pl ├── fa-compress_Ns.pl ├── fa-concat-on-id.pl ├── fa-correct_scaffold_Ns.pl ├── fa-deambiguate.pl ├── fa-deinterleave.pl ├── fa-dna_to_rna.pl ├── fa-dupe_velvet_high_cov_contigs.pl ├── fa-edit.pl ├── fa-estimate_insert_size.pl ├── fa-extract-few.pl ├── fa-extract.pl ├── fa-extract_by_exact_ids.pl ├── fa-extract_contig_ends.pl ├── fa-fake_illumina_reads.pl ├── fa-fake_qual_file.pl ├── fa-fake_sanger_reads.pl ├── fa-filter-size.pl ├── fa-find_pattern.pl ├── fa-find_primers_from_list.pl ├── fa-gc_content.pl ├── fa-get_sub_seq.pl ├── fa-grep.pl ├── fa-head.pl ├── fa-homopolymer_stats.pl ├── fa-interleave.pl ├── fa-interleaved_to_ssake.pl ├── fa-join.pl ├── fa-kmer_freqs.pl ├── fa-make_GC_plot_file.pl ├── fa-mlst.pl ├── fa-multi-concat.pl ├── fa-nr_to_r.pl ├── fa-one_line_seq.pl ├── fa-random_subset.pl ├── fa-re-partner.pl ├── fa-readStats.pl ├── fa-read_stats.pl ├── fa-remove_contaminants.pl ├── fa-remove_seq_with_N.pl ├── fa-remove_seqs_with_duplicate_id.pl ├── fa-rename.pl ├── fa-reorient.pl ├── fa-repair.pl ├── fa-revcom.pl ├── fa-run_SMP.pl ├── fa-scaffold_primers.pl ├── fa-show.pl ├── fa-size.pl ├── fa-sort.pl ├── fa-split.pl ├── fa-split_on_Ns.pl ├── fa-split_overlap.pl ├── fa-subseq.pl ├── fa-tile_contigs.pl ├── fa-to_fq.pl ├── fa-translate.pl ├── fa-unique.pl ├── fa-uniquest_kmer.pl ├── fast.pl ├── fastq2afg.pl ├── fq ├── fq-add_left_right_suffix.pl ├── fq-base_calls_by_pos.pl ├── fq-base_quality_report.pl ├── fq-check_GGCnG_problem.pl ├── fq-check_quality_values.pl ├── fq-clean.pl ├── fq-deinterleave.pl ├── fq-demux-paired.pl ├── fq-demux-single.pl ├── fq-estimate_insert_size.sh ├── fq-examine_quality.pl ├── fq-guess-encoding.pl ├── fq-head.pl ├── fq-interleave.pl ├── fq-multi_to_single_line.pl ├── fq-pre-process.pl ├── fq-quality-graph.pl ├── fq-quality_report.pl ├── fq-random_subset-pe.pl ├── fq-random_subset-se.pl ├── fq-re-partner.pl ├── fq-remove_clones.sh ├── fq-revcom.pl ├── fq-simulate_illumina_reads.pl ├── fq-singletons.pl ├── fq-size.pl ├── fq-sort_by_length.pl ├── fq-subseq.pl ├── fq-summarize.pl ├── fq-summarize_N_runs.pl ├── fq-to_afg.pl ├── fq-to_fa+qual.pl ├── fq-to_fa.pl ├── fq-trim-PE.pl ├── fq-trim.pl ├── fq-validate.pl ├── fq2fa ├── gb-join.pl ├── gb-rotate.pl └── re-number-contigs.pl ├── gbk-tools ├── gb-add_trans.pl ├── gb-codon-trna-checker.pl ├── gb-extract_upstream.pl ├── gb-mask_seqfeatures.pl ├── gb-split.pl.TWO_BUGS ├── gb-stats-quick.sh ├── gbk-to-sprot_fasta.pl ├── genbank2fasta.pl ├── genbank2gff.pl ├── genbank2krakenlib.pl.BIOPERL_PAIN ├── genbank2ptt.pl ├── genbank2tab.pl └── genbank_to_ptt.pl ├── gff-tools ├── Prokka.pm ├── aragorn2gff.pl ├── bed2gff3.pl ├── cmscantblout2gff.pl ├── gff3-extract_CDS.pl ├── gff3-extract_seq.pl ├── gff3-fix_refseq.pl ├── gff3-sort.pl ├── gff3-to-gbk.pl ├── glimmer2gff.pl ├── irf2gff.pl ├── signalp2gff.pl ├── tRNAscan2gff.pl └── trf2gff.pl ├── misc ├── 454-contig-grapher.pl ├── MP_splitter.pl ├── OLD.faa-cluster.pl ├── align-converter.pl ├── anno-clone.pl ├── assemble ├── bam-please.pl ├── cluster-two-protein-sets.pl ├── compare_pair_consequences.pl ├── contig-read-extender.pl ├── csfasta2fasta.pl ├── csv_to_html.pl ├── csv_to_tsv.pl ├── demux+sampsheet_to_folder.pl ├── dnadiff-addseqs.pl ├── ensembl-genbank-to-csv.pl ├── extract-orthologous-sequences.pl ├── fa-order_to_reference.pl ├── fa-to_agp+fsa.pl ├── faa-to-hmm.pl ├── gff2gff.pl ├── illumina-qseq-dir-to-fastq.pl ├── illumina-qseq-file-to-fastq.pl ├── illuminize.pl ├── listmath.pl ├── mdu-put_into_folders.pl ├── minimus2_easy.pl ├── needleman_wunsch.pl ├── nregs.pl ├── oases-choose_longest_transcript_per_locus.pl ├── oases-statistics.pl ├── orthomcl_to_csv.pl ├── orthomcl_to_flat_csv.pl ├── phantom2.pl ├── phred-to-454sanger.pl ├── proteinortho5-clade_genes.pl ├── proteinortho_to_svg.pl ├── reannotate.pl ├── simon_scaff_editor.pl ├── sra-batch-submit.pl ├── tree-from_contigs.pl ├── tsv_to_csv.pl └── webbify.pl ├── nesoni-tools ├── nesoni-all_nways.pl ├── nesoni-augment_report_with_CDS_affected.pl ├── nesoni-batch_run.pl ├── nesoni-big_tree.pl ├── nesoni-core_genome.pl ├── nesoni-core_snps.pl ├── nesoni-coverage_map.pl ├── nesoni-coverage_report.pl ├── nesoni-definite_snps.pl ├── nesoni-find_operons.pl ├── nesoni-fisher_to_proteins.pl ├── nesoni-import_ncbigenomes.pl ├── nesoni-nway_table.pl ├── nesoni-report_to_vcf.pl ├── nesoni-snps.pl ├── nesoni-snps_per_ftype.pl ├── nesoni-uniqueome.pl ├── nesoni2bamview.pl └── nesoni_nway-to-plink_map.pl ├── sam-tools ├── bam-view.pl ├── bam-view.pl.dev └── sam-pair_stats.pl ├── shrimp-tools ├── bam-avg_depth.pl ├── bam-base_distribution.pl ├── bwa-pe-snps.sh ├── consequences.py ├── fisher_diff.py ├── nway_diff.py ├── shrimp-exact_hits.pl ├── shrimp-unambig_hits.pl ├── shrimp2sam.pl ├── shrimp_consensus.py └── shrimp_run.py ├── uniprot-tools ├── uniprot-extract_family.pl ├── uniprot-to_fasta.pl └── uniprot_to_EC_fasta.pl └── velvet-tools ├── FixScaffs.pl ├── fa-clean_velvet_contig_names.pl ├── fa-extract_contig_ends.pl ├── runFixScaffsPreProcess.pl ├── transform_velvet_contig_afg.pl ├── velvet-bug_report.sh ├── velvet-estimate-exp_cov.pl 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