├── .github └── workflows │ └── python-package.yml ├── .gitignore ├── CHANGES.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── RELEASING.md ├── pyproject.toml ├── setup.cfg ├── setup.py ├── src └── nexus │ ├── __init__.py │ ├── __main__.py │ ├── checker.py │ ├── cli_util.py │ ├── commands │ ├── __init__.py │ ├── binary2multistate.py │ ├── check.py │ ├── combine.py │ ├── convert.py │ ├── deinterleave.py │ ├── describecharacter.py │ ├── describetaxa.py │ ├── edit.py │ ├── multistate2binary.py │ ├── randomise.py │ ├── tally.py │ └── trees.py │ ├── exceptions.py │ ├── handlers │ ├── __init__.py │ ├── data.py │ ├── taxa.py │ └── tree.py │ ├── reader.py │ ├── tools │ ├── __init__.py │ ├── binarise.py │ ├── check_zeros.py │ ├── combine_nexuses.py │ ├── multistatise.py │ ├── shufflenexus.py │ ├── sites.py │ ├── trees.py │ └── util.py │ ├── util.py │ └── writer.py └── tests ├── conftest.py ├── examples ├── example-beast.trees ├── example-characters.nex ├── example-comments.nex ├── example-translated.trees ├── example-wrapped-data.nex ├── example.nex ├── example.trees ├── example2.nex ├── example3.nex └── maddison_et_al.nex ├── regression ├── ape_random.trees ├── bad_chars_in_taxaname.trees ├── branchlengths-in-integers.trees ├── detranslate-beast-2.trees ├── detranslate-beast.trees ├── detranslate-with-dash.trees ├── edictor.nex ├── glottolog.trees ├── mesquite_formatted_branches.trees ├── mesquite_taxa_block.nex ├── mrbayes.trees ├── taxlabels.nex ├── tree_default_translate_with_comments.trees ├── tree_detranslate_chang.trees ├── tree_translate_mismatch.trees ├── tree_with_asterisk_in_taxa.trees └── white_space_in_matrix.nex ├── test_checker.py ├── test_cli.py ├── test_cli_util.py ├── test_handler_DataHandler.py ├── test_handler_GenericHandler.py ├── test_handler_TaxaHandler.py ├── test_handler_TreeHandler.py ├── test_maddison.py ├── test_reader.py ├── test_reader_manipulation.py ├── test_regressions.py ├── test_tools ├── test_binarise.py ├── 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