├── .github └── copilot-instructions.md ├── .gitignore ├── LICENSE.txt ├── README.md ├── conda_env.yml ├── docs ├── README.md ├── developing_domainator.md ├── esm_3b_foldseek.md ├── examples.md ├── file_formats.md ├── limitations_and_FAQ.md ├── media │ ├── Domainator_logo.svg │ ├── Overview_diagram.png │ ├── detective_Domainic_transparent_background.png │ ├── genome_mining_workflow.png │ ├── hmm_profile_comparison.png │ └── server_screenshot.png ├── server │ ├── README.md │ ├── adding_tools.md │ └── technical_overview.md └── web_server_design.md ├── domainator.def ├── domainator_esmologs.def ├── package.sh ├── pyproject.toml ├── scripts └── server │ └── generate_tool_schemas.py ├── src └── domainator │ ├── Bio │ ├── Data │ │ ├── CodonTable.py │ │ ├── IUPACData.py │ │ ├── SCOPData.py │ │ └── __init__.py │ ├── File.py │ ├── GenBank │ │ ├── Scanner.py │ │ ├── __init__.py │ │ └── utils.py │ ├── LICENSE.rst │ ├── Seq.py │ ├── SeqFeature.py │ ├── SeqIO │ │ ├── FastaIO.py │ │ ├── InsdcIO.py │ │ ├── InsdcIO_new.py │ │ ├── Interfaces.py │ │ ├── SwissIO.py │ │ ├── TabIO.py │ │ └── __init__.py │ ├── SeqRecord.py │ ├── SwissProt │ │ └── __init__.py │ └── __init__.py │ ├── Taxonomy │ └── __init__.py │ ├── __init__.py │ ├── build_projection.py │ ├── build_ssn.py │ ├── build_tree.py │ ├── color_genbank.py │ ├── color_table_to_legend.py │ ├── compare_contigs.py │ ├── cytoscape.py │ ├── data_matrix.py │ ├── deduplicate_genbank.py │ ├── domain_search.py │ ├── domainate.py │ ├── domainator_db_download.py │ ├── enum_report.py │ ├── extract_domains.py │ ├── extract_peptides.py │ ├── extract_unannotated.py │ ├── filter_domains.py │ ├── foldseek.py │ ├── genbank_to_fasta.py │ ├── hmmer_build.py │ ├── hmmer_compare.py │ ├── hmmer_report.py │ ├── hmmer_search.py │ ├── hmmer_select.py │ ├── matrix_report.py │ ├── partition_seqfile.py │ ├── partition_seqids.py │ ├── plot_contigs.py │ ├── select_by_cds.py │ ├── select_by_contig.py │ ├── seq_dist.py │ ├── server │ ├── __init__.py │ ├── app.py │ ├── cli.py │ ├── config.py │ ├── file_manager.py │ ├── schemas │ │ ├── archived │ │ │ └── partition_seqfile.json │ │ └── domainator │ │ │ ├── build_projection.json │ │ │ ├── build_ssn.json │ │ │ ├── build_tree.json │ │ │ ├── color_genbank.json │ │ │ ├── color_table_to_legend.json │ │ │ ├── compare_contigs.json │ │ │ ├── deduplicate_genbank.json │ │ │ ├── domain_search.json │ │ │ ├── domainate.json │ │ │ ├── domainator_db_download.json │ │ │ ├── enum_report.json │ │ │ ├── extract_domains.json │ │ │ ├── extract_peptides.json │ │ │ ├── extract_unannotated.json │ │ │ ├── filter_domains.json │ │ │ ├── genbank_to_fasta.json │ │ │ ├── hmmer_build.json │ │ │ ├── hmmer_compare.json │ │ │ ├── hmmer_report.json │ │ │ ├── hmmer_search.json │ │ │ ├── hmmer_select.json │ │ │ ├── matrix_report.json │ │ │ ├── plot_contigs.json │ │ │ ├── select_by_cds.json │ │ │ ├── select_by_contig.json │ │ │ ├── seq_dist.json │ │ │ ├── summary_report.json │ │ │ ├── transform_matrix.json │ │ │ └── trim_contigs.json │ ├── static │ │ ├── Domainator_logo.svg │ │ ├── app.js │ │ ├── domainator_glyph.svg │ │ ├── styles.css │ │ └── tool-category-config.json │ ├── templates │ │ └── index.html │ ├── tool_executor.py │ ├── tool_registry.py │ └── workflows │ │ └── genome_annotation.py │ ├── summary_report.py │ ├── transform_matrix.py │ ├── trim_contigs.py │ └── utils.py └── test ├── data ├── 206.gb ├── CcdB.hmm ├── CcdB.hmm.h3f ├── CcdB.hmm.h3i ├── CcdB.hmm.h3m ├── CcdB.hmm.h3p ├── CuSOD_enum_report_test.gb ├── FeSOD_20.fasta ├── FeSOD_20.gb ├── FeSOD_20_pfam.gb ├── FeSOD_dist.dense.hdf5 ├── FeSOD_dist.sparse.hdf5 ├── FeSOD_dist.tsv ├── FeSOD_metadata.tsv ├── FeSOD_pfam.hmm ├── FeSOD_score_dist.newick ├── FeSOD_score_dist.tsv ├── FeSOD_score_dist.xgmml ├── JABFVH010000506_extraction.gb ├── MT_nbs.enum_report.tsv ├── MT_nbs.gb ├── Peptidase_M28.hmm ├── Peptidase_M28.hmm.h3f ├── Peptidase_M28.hmm.h3i ├── Peptidase_M28.hmm.h3m ├── Peptidase_M28.hmm.h3p ├── Polymorphism_feature.gb ├── SPR.hmm ├── Staph_phages.gb ├── bacillus_phage_SPR.gb ├── bacillus_phage_SPR_with_annotations.gb ├── bacillus_phage_SPR_with_annotations_reversed.gb ├── bin3.sparse.hdf5 ├── bin3.sparse.tsv ├── bin3.tsv ├── ccdb.gb ├── color_domain_search_test.gb ├── color_specification.tsv ├── color_table_123.tsv ├── domain_search_test_out1.gb ├── domain_search_test_out2.gb ├── domain_search_test_out3.gb ├── domain_search_translate_out.gb ├── empty.gb ├── enum_report_html_max_size_out.html ├── enum_report_html_out.html ├── enum_report_html_out_quote_escape.html ├── extract_peptides_test_1_out.gb ├── extract_peptides_test_2.gb ├── foldseek │ ├── FeSOD │ ├── FeSOD.dbtype │ ├── FeSOD.index │ ├── FeSOD.lookup │ ├── FeSOD_20.3di.fasta │ ├── FeSOD_20.fasta │ ├── FeSOD_h │ ├── FeSOD_h.dbtype │ ├── FeSOD_h.index │ ├── FeSOD_ss │ ├── FeSOD_ss.dbtype │ └── FeSOD_ss.index ├── metadata_FeSOD_20.tsv ├── pDONR201.fasta ├── pDONR201.gb ├── pDONR201_domainator_circular.gb ├── pDONR201_empty.gb ├── pDONR201_genemark.gb ├── pDONR201_genemark.gff ├── pDONR201_multi.fasta ├── pDONR201_multi_genemark.gb ├── pDONR201_multi_genemark.gff ├── pDONR201_multi_genemark_clipped_domainator.gb ├── pDONR201_multi_genemark_domainator.gb ├── pDONR201_multi_genemark_domainator_multi_hmm.gb ├── pDONR201_multi_genemark_domainator_multi_hmm_2.gb ├── pDONR201_multi_subset.txt ├── pDONR201_multigenemark_partition.gb ├── pDONR201_no_CDSs.gb ├── pDONR201_partly_CDSs.gb ├── pDONR201_pseudo.gb ├── pDONR_201_domain_search.gb ├── pDONR_201_domain_search_long_annotations.gb ├── pDONR_201_domainator.gb ├── pDONR_201_domainator_domain_reorder.gb ├── pDONR_201_hmm_scores.tsv ├── pdonr_hmms.hmm ├── pdonr_hmms_1.hmm ├── pdonr_hmms_2.hmm ├── pdonr_peptides.fasta ├── saccharomyces_defense_finder.hmm ├── saccharomyces_extraction.gb ├── saccharomyces_extraction_circular.gb ├── score3.sparse.tsv ├── score4.sparse.tsv ├── scorefull.dense.hdf5 ├── scorefull.tsv ├── simple_genpept.gb ├── simple_genpept_contigs.txt ├── simple_genpept_equals_second_line.gb ├── simple_genpept_quote_name.gb ├── ssn_FeSOD.sparse.xgmml ├── ssn_FeSOD.xgmml ├── ssn_FeSOD_clusters.tsv ├── ssn_FeSOD_clusters_header.tsv ├── swissprot_CuSOD_subset.fasta ├── taxdmp │ ├── delnodes.dmp │ ├── merged.dmp │ ├── names.dmp │ ├── nodes.dmp │ └── taxdump.tar.gz ├── test_matrix.dense.hdf5 ├── test_matrix.dense.tsv ├── test_matrix.sparse.hdf5 └── thymidylate_synthase.fasta ├── helpers.py ├── server ├── __init__.py ├── conftest.py ├── test_app_files.py ├── test_app_jobs.py ├── test_app_tools.py ├── test_domainator_schemas.py ├── test_file_manager.py ├── test_tool_executor.py └── test_tool_registry.py ├── test_SeqFeature.py ├── test_build_projection.py ├── test_build_ssn.py ├── test_build_tree.py ├── test_color_genbank.py ├── test_color_table_to_legend.py ├── test_compare_contigs.py ├── test_data_matrix.py ├── test_deduplicate_genbank.py ├── test_domain_search.py ├── test_domainate.py ├── test_domainator_db_download.py ├── test_enum_report.py ├── test_extract_domains.py ├── 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