├── .github └── workflows │ ├── package.yml │ ├── requirements.txt │ └── test.yml ├── .gitignore ├── .gitmodules ├── .readthedocs.yaml ├── CHANGELOG.md ├── CMakeLists.txt ├── CONTRIBUTING.md ├── COPYING ├── README.md ├── docs ├── .gitignore ├── Makefile ├── _static │ ├── js │ │ └── custom-icon.js │ └── json │ │ └── switcher.json ├── api │ ├── aligner.rst │ ├── alignment.rst │ ├── gapped_sequence.rst │ ├── guide_tree.rst │ ├── index.rst │ ├── sequence.rst │ └── utilities.rst ├── conf.py ├── guide │ ├── changes.md │ ├── contributing.md │ ├── copyright.rst │ ├── index.rst │ └── install.rst ├── index.rst ├── make.bat └── requirements.txt ├── include └── famsa │ ├── __init__.pxd │ ├── core │ ├── __init__.pxd │ ├── io_service.pxd │ ├── params.pxd │ ├── profile.pxd │ ├── scoring_matrix.pxd │ ├── sequence.pxd │ └── version.pxd │ ├── msa.pxd │ ├── tree │ ├── __init__.pxd │ ├── abstract_tree_generator.pxd │ ├── guide_tree.pxd │ └── newick_parser.pxd │ └── utils │ ├── __init__.pxd │ ├── log.pxd │ └── memory_monotonic.pxd ├── patches ├── NewickParser.h.patch ├── memory_monotonic.h.patch ├── msa.cpp.patch ├── msa.h.patch ├── msa_refinement.cpp.patch ├── sequence.cpp.patch └── sequence.h.patch ├── pkg └── aur │ └── PKGBUILD.in ├── pyproject.toml └── src ├── CMakeLists.txt ├── FAMSA └── CMakeLists.txt ├── pyfamsa ├── CMakeLists.txt ├── __init__.py ├── _famsa.pxd ├── _famsa.pyi ├── _famsa.pyx ├── py.typed └── tests │ ├── __init__.py │ ├── __main__.py │ ├── data │ ├── __init__.py │ ├── adeno_fiber.faa │ ├── adeno_fiber.p1.afa │ ├── adeno_fiber.p2.afa │ ├── adeno_fiber.sl.afa │ ├── adeno_fiber.sl.nwk │ ├── adeno_fiber.upgma.afa │ ├── adeno_fiber.upgma.nwk │ ├── adeno_fiber.upgma.pp.afa │ ├── hemopexin.faa │ ├── hemopexin.medoid-nj.afa │ ├── hemopexin.medoid-nj.nwk │ ├── hemopexin.medoid-sl.afa │ ├── hemopexin.medoid-sl.nwk │ ├── hemopexin.medoid-slink.nwk │ ├── hemopexin.medoid-upgma.afa │ └── hemopexin.medoid-upgma.nwk │ ├── fasta.py │ ├── requirements.txt │ ├── test_aligner.py │ ├── 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