CHANGELOG.md
CITATION.cff
LICENSE.txt
MANIFEST.in
MIGRATION.md
README.md
pyproject.toml
setup.py
rust/Cargo.lock
rust/Cargo.toml
rust/src/bgzf_compress.rs
rust/src/bgzf_scan.rs
rust/src/lib.rs
rust/src/parser.rs
src/domainator/__init__.py
src/domainator/__main__.py
src/domainator/_hmm_kernels.py
src/domainator/_mp.py
src/domainator/bgzf_compress.py
src/domainator/build_projection.py
src/domainator/build_ssn.py
src/domainator/build_tree.py
src/domainator/clean_sequences.py
src/domainator/color_genbank.py
src/domainator/color_table_to_legend.py
src/domainator/colors.py
src/domainator/compare_contigs.py
src/domainator/cytoscape.py
src/domainator/data_matrix.py
src/domainator/db_download.py
src/domainator/db_index.py
src/domainator/dedup.py
src/domainator/deduplicate_genbank.py
src/domainator/domain_search.py
src/domainator/domainate.py
src/domainator/edge_types.py
src/domainator/enum_report.py
src/domainator/errors.py
src/domainator/expr.py
src/domainator/external.py
src/domainator/extract_domains.py
src/domainator/extract_peptides.py
src/domainator/extract_unannotated.py
src/domainator/filter_domains.py
src/domainator/find_features.py
src/domainator/foldseek.py
src/domainator/format_db.py
src/domainator/genbank.py
src/domainator/genbank_to_fasta.py
src/domainator/hmmer_build.py
src/domainator/hmmer_compare.py
src/domainator/hmmer_report.py
src/domainator/hmmer_search.py
src/domainator/hmmer_select.py
src/domainator/hmmio.py
src/domainator/infernal_build.py
src/domainator/kmer_dist.py
src/domainator/lean_record.py
src/domainator/location_ops.py
src/domainator/locations.py
src/domainator/matrix_output.py
src/domainator/matrix_report.py
src/domainator/model.py
src/domainator/offsets.py
src/domainator/output_guardrails.py
src/domainator/outputs.py
src/domainator/partial.py
src/domainator/plot_contigs.py
src/domainator/report_columns.py
src/domainator/report_html.py
src/domainator/rotate_contigs.py
src/domainator/select_by_cds.py
src/domainator/select_by_contig.py
src/domainator/select_by_coord.py
src/domainator/seq_dist.py
src/domainator/seqio.py
src/domainator/sort_contigs.py
src/domainator/sparse_scores.py
src/domainator/sparsify.py
src/domainator/split_by_cluster.py
src/domainator/ssn_bundle.py
src/domainator/ssn_edges.py
src/domainator/ssn_hierarchy.py
src/domainator/ssn_navigator.py
src/domainator/structure_dist.py
src/domainator/structure_domainate.py
src/domainator/structure_lib.py
src/domainator/structure_search.py
src/domainator/structure_to_genbank.py
src/domainator/summary_report.py
src/domainator/table_writers.py
src/domainator/text_plot.py
src/domainator/transform_matrix.py
src/domainator/trim_contigs.py
src/domainator/viewer.py
src/domainator/viewer_bundle.py
src/domainator/viewer_html.py
src/domainator.egg-info/PKG-INFO
src/domainator.egg-info/SOURCES.txt
src/domainator.egg-info/dependency_links.txt
src/domainator.egg-info/entry_points.txt
src/domainator.egg-info/requires.txt
src/domainator.egg-info/top_level.txt
src/domainator/cli/__init__.py
src/domainator/cli/common.py
src/domainator/cli/completion.py
src/domainator/cli/doctor.py
src/domainator/cli/manifest.py
src/domainator/cli/registry.py
src/domainator/taxonomy/__init__.py
src/domainator/taxonomy/ncbi.py
src/domainator/taxonomy/records.py
src/domainator/viewer_app/viewer.css
src/domainator/viewer_app/viewer.html
src/domainator/viewer_app/js/viewer.js
src/domainator/viewer_app/js/common/appearance.js
src/domainator/viewer_app/js/common/bundle_io.js
src/domainator/viewer_app/js/common/canvas_view.js
src/domainator/viewer_app/js/common/color_picker.js
src/domainator/viewer_app/js/common/colors.js
src/domainator/viewer_app/js/common/column_charts.js
src/domainator/viewer_app/js/common/controls.js
src/domainator/viewer_app/js/common/export.js
src/domainator/viewer_app/js/common/gradient_stops.js
src/domainator/viewer_app/js/common/metadata.js
src/domainator/viewer_app/js/common/metadata_table.js
src/domainator/viewer_app/js/common/selection_presets.js
src/domainator/viewer_app/js/common/session_state.js
src/domainator/viewer_app/js/common/shapes.js
src/domainator/viewer_app/js/common/svg_context.js
src/domainator/viewer_app/js/common/table_editing.js
src/domainator/viewer_app/js/views/projection/projection.js
src/domainator/viewer_app/js/views/projection/view.js
src/domainator/viewer_app/js/views/ssn/cluster_view.js
src/domainator/viewer_app/js/views/ssn/controls.js
src/domainator/viewer_app/js/views/ssn/extraction.js
src/domainator/viewer_app/js/views/ssn/layout_core.js
src/domainator/viewer_app/js/views/ssn/layout_worker.js
src/domainator/viewer_app/js/views/ssn/layouts.js
src/domainator/viewer_app/js/views/ssn/slider.js
src/domainator/viewer_app/js/views/ssn/split_chart.js
src/domainator/viewer_app/js/views/ssn/split_chart_hover.js
src/domainator/viewer_app/js/views/ssn/view.js
src/domainator/viewer_app/js/views/tree/controls.js
src/domainator/viewer_app/js/views/tree/msa.js
src/domainator/viewer_app/js/views/tree/render.js
src/domainator/viewer_app/js/views/tree/rooting.js
src/domainator/viewer_app/js/views/tree/tree.js
src/domainator/viewer_app/js/views/tree/view.js
src/domainator/web/common/charts.js
src/domainator/web/common/download.js
src/domainator/web/common/hierarchy.js
src/domainator/web/common/line_chart.js
src/domainator/web/common/pack.js
src/domainator/web/common/panels.js
src/domainator/web/common/payload.js
src/domainator/web/common/report.css
src/domainator/web/common/table.js
src/domainator/web/reports/matrix_report.html
src/domainator/web/reports/matrix_report.js
src/domainator/web/reports/plot_contigs.html
src/domainator/web/reports/plot_contigs.js
src/domainator/web/reports/summary_report.html
src/domainator/web/reports/summary_report.js
src/domainator/web/reports/table_report.html
src/domainator/web/reports/table_report.js
test/test_agent_outputs.py
test/test_annotation_selection.py
test/test_build_projection.py
test/test_build_ssn.py
test/test_build_tree.py
test/test_cds_selection.py
test/test_clean_sequences.py
test/test_cli.py
test/test_color_genbank.py
test/test_color_table_to_legend.py
test/test_compare_contigs.py
test/test_coordinates.py
test/test_cytoscape.py
test/test_data_matrix.py
test/test_db_download.py
test/test_db_index.py
test/test_dedup.py
test/test_deduplicate_genbank.py
test/test_defaults_match_cli.py
test/test_docs_commands.py
test/test_domain_search.py
test/test_domainate.py
test/test_enum_report.py
test/test_external.py
test/test_extract_domains.py
test/test_extract_peptides.py
test/test_extract_unannotated.py
test/test_filter_domains.py
test/test_find_features.py
test/test_foldseek.py
test/test_format_db.py
test/test_genbank.py
test/test_genbank_to_fasta.py
test/test_hmmer_build.py
test/test_hmmer_compare.py
test/test_hmmer_report.py
test/test_hmmer_search.py
test/test_hmmer_select.py
test/test_infernal_build.py
test/test_kmer_dist.py
test/test_lean_record.py
test/test_library_api.py
test/test_list_arguments.py
test/test_location_ops.py
test/test_manifest.py
test/test_matrix_report.py
test/test_mp.py
test/test_ncbi_taxonomy.py
test/test_outputs.py
test/test_partition.py
test/test_plot_contigs.py
test/test_region_naming.py
test/test_report_browser.py
test/test_report_columns.py
test/test_report_html.py
test/test_rotate_contigs.py
test/test_select_by_cds.py
test/test_select_by_contig.py
test/test_select_by_coord.py
test/test_seq_dist.py
test/test_sort_contigs.py
test/test_sparsify.py
test/test_split_by_cluster.py
test/test_ssn_edges.py
test/test_ssn_hierarchy.py
test/test_ssn_viewer_browser.py
test/test_ssn_viewer_js.py
test/test_structure_dist.py
test/test_structure_domainate.py
test/test_structure_lib.py
test/test_structure_reseek.py
test/test_structure_search.py
test/test_structure_to_genbank.py
test/test_summary_report.py
test/test_taxonomy_filters.py
test/test_taxonomy_records.py
test/test_transform_matrix.py
test/test_trim_contigs.py
test/test_utils.py
test/test_viewer.py
test/test_viewer_appearance_browser.py
test/test_viewer_appearance_js.py
test/test_viewer_image_export_browser.py
test/test_viewer_projection_browser.py
test/test_viewer_rooting_js.py
test/test_viewer_tree_browser.py