├── .github ├── dependabot.yml └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── .gitignore ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── ReleaseNotes.txt ├── docs ├── Makefile ├── api.rst ├── conf.py ├── filter.rst ├── gene.rst ├── genome.rst ├── ham.rst ├── iHam.rst ├── index.rst ├── make.bat ├── mapper.rst ├── taxonomy.rst ├── treeprofile.rst └── utils.rst ├── example ├── TreeProfileHOG:0355161.html ├── TreeProfileHOG:0359282.html ├── run_hog_queries.py ├── run_iHam.py ├── run_pyham_using_oma_server.py ├── run_treeProfile.py ├── simpleEx.orthoxml └── simpleEx.phyloxml ├── fabfile.py ├── help.pdf ├── pyham ├── TreeProfile.py ├── __init__.py ├── abstractgene.py ├── genome.py ├── ham.py ├── iham.py ├── mapper.py ├── parsers.py ├── taxonomy.py └── utils.py ├── requirements.txt ├── setup.cfg ├── setup.py ├── test-requirements.txt └── tests ├── data ├── Conflict1 │ ├── hog.orthoxml │ ├── note.txt │ └── tree.nwk ├── SimpleEx_complexParalogGetHOGS3format.xml ├── birds.nwk ├── birds.orthoxml ├── hogvisEx.orthoxml ├── multiple_duplication_example.xml ├── p53_augmented.orthoxml ├── p53_augmented_speciestree.phyloxml ├── paralogs_only_inside_og.nwk ├── paralogs_only_inside_og.orthoxml ├── paralogs_only_toplevel_og.nwk ├── paralogs_only_toplevel_og.orthoxml ├── parser │ ├── Info.txt │ ├── conflict_duplication_children.orthoxml │ └── tree.newick ├── simpleEx.nwk ├── simpleEx.orthoxml ├── simpleEx.phyloxml ├── simpleExNoCladeName.phyloxml ├── simpleExNoName.nwk ├── simpleExNoName.phyloxml └── simpleEx_complexParalogs.orthoxml ├── functional_test.py ├── test_abstractgene.py ├── test_annotated_bird_orthoxml_problem.py ├── test_conflict.py ├── test_genome.py ├── test_ham.py ├── test_iham.py ├── test_mapper.py ├── test_orthoxmlparser.py ├── test_taxonomy.py ├── test_treeprofile.py └── test_utils.py /.github/dependabot.yml: -------------------------------------------------------------------------------- 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