LICENSE
README.md
pyproject.toml
src/egt/__init__.py
src/egt/aggregate_filechecker_benchmarks.py
src/egt/aggregate_filesizes.py
src/egt/algs_split_across_scaffolds.py
src/egt/annotate_sample_df.py
src/egt/arthropoda_umap_clusters.py
src/egt/bokeh_helper.py
src/egt/build_family_naming_map.py
src/egt/cli.py
src/egt/count_unique_changes_per_branch.py
src/egt/custom_taxonomy.py
src/egt/defining_features.py
src/egt/defining_features_plot.py
src/egt/defining_features_plotRBH.py
src/egt/defining_features_qc_plots.py
src/egt/dispersal_panel_style.py
src/egt/divergence_vs_dispersal.py
src/egt/entanglement_browse.py
src/egt/entanglement_go_enrich.py
src/egt/fourier_of_rates.py
src/egt/fourier_spectral_background.py
src/egt/get_assembly_sizes.py
src/egt/go_subcommands.py
src/egt/join_supplementary_tables.py
src/egt/newick_to_common_ancestors.py
src/egt/odol_annotate_blast.py
src/egt/palette.py
src/egt/palette_preview.py
src/egt/perspchrom_df_to_tree.py
src/egt/phylotreeumap.py
src/egt/phylotreeumap_plotdfs.py
src/egt/phylotreeumap_subsample.py
src/egt/phylotreeumap_testpixels.py
src/egt/pigeonhole_check.py
src/egt/plot_alg_dispersal.py
src/egt/plot_alg_fusions.py
src/egt/plot_branch_stats_advanced.py
src/egt/plot_branch_stats_tree.py
src/egt/plot_branch_stats_tree_pair.py
src/egt/plot_branch_stats_vs_time.py
src/egt/plot_chrom_number_vs_changes.py
src/egt/plot_collapsed_tree.py
src/egt/plot_decay_many_species.py
src/egt/plot_decay_pairwise_steps.py
src/egt/plot_fourier_support_vs_time.py
src/egt/plot_tree_changes.py
src/egt/pull_entries_from_yaml.py
src/egt/rbh_tools.py
src/egt/taxid_tools.py
src/egt/taxids_to_newick.py
src/egt/umap_taxonomy_clusters.py
src/egt.egg-info/PKG-INFO
src/egt.egg-info/SOURCES.txt
src/egt.egg-info/dependency_links.txt
src/egt.egg-info/entry_points.txt
src/egt.egg-info/requires.txt
src/egt.egg-info/top_level.txt
src/egt/_testing/__init__.py
src/egt/_testing/gb_roundtrip.py
src/egt/_testing/grid_verify_coo.py
src/egt/_vendor/__init__.py
src/egt/_vendor/odp_plotting_functions.py
src/egt/data/__init__.py
src/egt/data/paper_palette.yaml
src/egt/data/paper_palette_simple.yaml
src/egt/go/__init__.py
src/egt/go/benchmark_dispatch.py
src/egt/go/enrichment.py
src/egt/go/io.py
src/egt/go/pair_coenrich.py
src/egt/go/stats.py
src/egt/go/sweep.py
src/egt/go/benchmarks/__init__.py
src/egt/go/benchmarks/alg_structure.py
src/egt/go/benchmarks/camps.py
src/egt/go/benchmarks/goatools_ref.py
src/egt/go/benchmarks/simakov.py
src/egt/go/plots/__init__.py
src/egt/go/plots/enrich.py
src/egt/go/plots/pair_coenrich.py
src/egt/go/plots/pair_distance.py
src/egt/go/plots/volcano.py
src/egt/legacy/__init__.py
src/egt/legacy/defining_features_plot2.py
src/egt/legacy/plot_alg_fusions_v1.py
src/egt/legacy/plot_alg_fusions_v2.py
tests/test_aggregate_filechecker_benchmarks.py
tests/test_aggregate_filesizes.py
tests/test_algs_split_across_scaffolds.py
tests/test_annotate_sample_df.py
tests/test_arthropoda_umap_clusters.py
tests/test_bokeh_helper.py
tests/test_build_family_naming_map.py
tests/test_cli.py
tests/test_coo_construction.py
tests/test_coo_integrity.py
tests/test_count_unique_changes_per_branch.py
tests/test_custom_taxonomy_policy.py
tests/test_defining_features_edge_cases.py
tests/test_defining_features_flags.py
tests/test_defining_features_output.py
tests/test_defining_features_plot.py
tests/test_defining_features_plot2_main.py
tests/test_defining_features_plotRBH.py
tests/test_defining_features_qc_plots.py
tests/test_dispersal.py
tests/test_dispersal_panel_style.py
tests/test_distance_computation.py
tests/test_divergence_vs_dispersal.py
tests/test_end_to_end_fixture.py
tests/test_entanglement_browse.py
tests/test_entanglement_go_enrich.py
tests/test_fourier_of_rates.py
tests/test_fourier_spectral_background.py
tests/test_gb_roundtrip.py
tests/test_get_assembly_sizes.py
tests/test_go_benchmark_camps.py
tests/test_go_benchmark_goatools_ref.py
tests/test_go_benchmark_simakov.py
tests/test_go_benchmarks.py
tests/test_go_cli.py
tests/test_go_coverage_edges.py
tests/test_go_coverage_fillers.py
tests/test_go_dotplot_variants.py
tests/test_go_enrichment.py
tests/test_go_io.py
tests/test_go_pair_coenrich.py
tests/test_go_plots.py
tests/test_go_stats.py
tests/test_go_sweep.py
tests/test_go_sweep_coverage.py
tests/test_join_supplementary_tables.py
tests/test_legacy_plot_alg_fusions_v1.py
tests/test_legacy_plot_alg_fusions_v2.py
tests/test_newick_taxidtree.py
tests/test_newick_taxidtree_more.py
tests/test_newick_to_common_ancestors_helpers.py
tests/test_newick_to_common_ancestors_main.py
tests/test_odol_annotate_blast.py
tests/test_odp_plotting_functions.py
tests/test_palette.py
tests/test_palette_preview.py
tests/test_perspchrom_df_to_tree_coloc_array.py
tests/test_perspchrom_df_to_tree_helpers.py
tests/test_phylotreeumap.py
tests/test_phylotreeumap_additional.py
tests/test_phylotreeumap_helpers.py
tests/test_phylotreeumap_more_helpers.py
tests/test_phylotreeumap_plotdfs_helpers.py
tests/test_phylotreeumap_plotdfs_more.py
tests/test_phylotreeumap_rendering.py
tests/test_phylotreeumap_subsample.py
tests/test_phylotreeumap_testpixels.py
tests/test_pigeonhole_check.py
tests/test_plot_alg_dispersal.py
tests/test_plot_alg_fusions_helpers.py
tests/test_plot_alg_fusions_tree_methods.py
tests/test_plot_branch_stats_advanced.py
tests/test_plot_branch_stats_tree.py
tests/test_plot_branch_stats_tree_pair.py
tests/test_plot_branch_stats_vs_time_helpers.py
tests/test_plot_branch_stats_vs_time_main.py
tests/test_plot_chrom_number_vs_changes.py
tests/test_plot_collapsed_tree.py
tests/test_plot_decay_many_species.py
tests/test_plot_decay_pairwise_steps.py
tests/test_plot_fourier_support_vs_time.py
tests/test_plot_tree_changes.py
tests/test_pull_entries_from_yaml.py
tests/test_rbh_parsing.py
tests/test_rbh_tools_more.py
tests/test_sparse_roundtrip.py
tests/test_sparse_vs_legacy.py
tests/test_taxid_tools.py
tests/test_taxids_to_newick.py