├── README.md ├── doc ├── Install_Programs.txt ├── Mods_to_programs.txt └── Run_Annotation.txt ├── scripts ├── EditAlignFile4RepeatedGenes.pl ├── GeneStats.pl ├── GeneStats.py ├── PerlLib │ ├── Accuracy_Eval.pm │ ├── BHStats.pm │ ├── CdbTools.pm │ ├── EVM_output_parser.pm │ ├── Fasta_reader.pm │ ├── GFF3_to_geneobjs.pm │ ├── GFF3_utils.pm │ ├── GFF_maker.pm │ ├── GTF_to_geneobjs.pm │ ├── GTF_utils.pm │ ├── Gene_obj.pm │ ├── Gene_obj_comparator.pm │ ├── Gene_obj_indexer.pm │ ├── Gene_ontology.pm │ ├── Gene_validator.pm │ ├── Longest_orf.pm │ ├── Nuc_translator.pm │ ├── Overlap_piler.pm │ ├── SnSp │ │ ├── SnSp_analysis.pm │ │ ├── SnSp_analysis_entry.pm │ │ ├── SnSp_analysis_manager.pm │ │ └── TFPN.pm │ └── TiedHash.pm ├── SNAP_output_to_gff3.pl ├── check_nucleotide_fasta_file_v1.py ├── cleanMAKER.py ├── createRepeatLandscape_modified4RepeatedGenes.pl ├── fasta-splitter.pl ├── filter_EVM_files.py ├── filter_ids.py ├── get_PASA_for__prepare_golden_genes.py ├── get_PASA_validation_stats.sh ├── get_filtered_EVM_files.py ├── load_EVM_to_SQLite3.py └── transposonPSI_mod.pl └── src ├── Augustus_Prediction.sh ├── Augustus_Training.sh ├── BLAST_Batch.sh ├── CD_HIT.sh ├── EVidenceModeler.sh ├── Examine_Strand_Specificity.sh ├── Genemark-ES.sh ├── GoldenGenes.sh ├── HHBLITS.sh ├── MAKER_PROTEIN_maker_bopts.ctl ├── MAKER_PROTEIN_maker_exe.ctl ├── MAKER_PROTEIN_maker_opts.ctl ├── MAKER_PROTEIN_run_MAKER.sh ├── MAKER_PROTEIN_setup_maker_Batch.sh ├── PASA.sh ├── PASA_alignAssembly.config ├── PBS_array_header.sh ├── PBS_header.sh ├── RepeatAnalysis.sh ├── SNAP.sh ├── SeqClean.sh ├── TransposonPSI.sh ├── TrinityDN.sh ├── TrinityGG.sh ├── env.sh ├── evm_weights.txt ├── exonerate_five_prime.pssm ├── exonerate_three_prime.pssm ├── gm_key └── workflow_setup.sh /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TimothyStephens/Dinoflagellate_Annotation_Workflow/HEAD/README.md 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