CHANGELOG.md
CONTRIBUTING.md
COPYING
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
./pyfamsa/_famsa.pyx
./vendor/FAMSA/libs/mimalloc/static.cpp
./vendor/FAMSA/src/msa.cpp
./vendor/FAMSA/src/msa_refinement.cpp
./vendor/FAMSA/src/core/params.cpp
./vendor/FAMSA/src/core/profile.cpp
./vendor/FAMSA/src/core/profile_par.cpp
./vendor/FAMSA/src/core/profile_seq.cpp
./vendor/FAMSA/src/core/queues.cpp
./vendor/FAMSA/src/core/sequence.cpp
./vendor/FAMSA/src/lcs/lcsbp.cpp
./vendor/FAMSA/src/lcs/lcsbp_classic.cpp
./vendor/FAMSA/src/tree/AbstractTreeGenerator.cpp
./vendor/FAMSA/src/tree/Clustering.cpp
./vendor/FAMSA/src/tree/DistanceCalculator.cpp
./vendor/FAMSA/src/tree/FastTree.cpp
./vendor/FAMSA/src/tree/GuideTree.cpp
./vendor/FAMSA/src/tree/MSTPrim.cpp
./vendor/FAMSA/src/tree/NeighborJoining.cpp
./vendor/FAMSA/src/tree/NewickParser.cpp
./vendor/FAMSA/src/tree/SingleLinkage.cpp
./vendor/FAMSA/src/tree/UPGMA.cpp
./vendor/FAMSA/src/utils/log.cpp
./vendor/FAMSA/src/utils/timer.cpp
./vendor/FAMSA/src/utils/utils.cpp
include/famsa/__init__.pxd
include/famsa/msa.pxd
include/famsa/core/__init__.pxd
include/famsa/core/io_service.pxd
include/famsa/core/params.pxd
include/famsa/core/profile.pxd
include/famsa/core/sequence.pxd
include/famsa/core/version.pxd
include/famsa/tree/__init__.pxd
include/famsa/tree/abstract_tree_generator.pxd
include/famsa/tree/guide_tree.pxd
include/famsa/tree/newick_parser.pxd
include/famsa/utils/__init__.pxd
include/famsa/utils/log.pxd
include/famsa/utils/memory_monotonic.pxd
patches/NewickParser.h.patch
patches/memory_monotonic.h.patch
patches/msa.cpp.patch
patches/msa.h.patch
patches/sequence.cpp.patch
patches/sequence.h.patch
pyfamsa/__init__.py
pyfamsa/_famsa.pxd
pyfamsa/_famsa.pyi
pyfamsa/_famsa.pyx
pyfamsa/_version.py
pyfamsa/py.typed
pyfamsa.egg-info/PKG-INFO
pyfamsa.egg-info/SOURCES.txt
pyfamsa.egg-info/dependency_links.txt
pyfamsa.egg-info/not-zip-safe
pyfamsa.egg-info/top_level.txt
pyfamsa/tests/__init__.py
pyfamsa/tests/__main__.py
pyfamsa/tests/fasta.py
pyfamsa/tests/requirements.txt
pyfamsa/tests/test_aligner.py
pyfamsa/tests/test_doctest.py
pyfamsa/tests/test_sequence.py
pyfamsa/tests/data/__init__.py
pyfamsa/tests/data/adeno_fiber.faa
pyfamsa/tests/data/adeno_fiber.sl.afa
pyfamsa/tests/data/adeno_fiber.sl.nwk
pyfamsa/tests/data/adeno_fiber.upgma.afa
pyfamsa/tests/data/adeno_fiber.upgma.nwk
pyfamsa/tests/data/hemopexin.faa
pyfamsa/tests/data/hemopexin.medoid-nj.afa
pyfamsa/tests/data/hemopexin.medoid-nj.nwk
pyfamsa/tests/data/hemopexin.medoid-sl.afa
pyfamsa/tests/data/hemopexin.medoid-sl.nwk
pyfamsa/tests/data/hemopexin.medoid-slink.nwk
pyfamsa/tests/data/hemopexin.medoid-upgma.afa
pyfamsa/tests/data/hemopexin.medoid-upgma.nwk
vendor/FAMSA/LICENSE
vendor/FAMSA/README.md
vendor/FAMSA/makefile
vendor/FAMSA/libs/atomic_wait/atomic_wait
vendor/FAMSA/libs/atomic_wait/barrier
vendor/FAMSA/libs/atomic_wait/latch
vendor/FAMSA/libs/atomic_wait/semaphore
vendor/FAMSA/libs/libdeflate/.gitignore
vendor/FAMSA/libs/libdeflate/COPYING
vendor/FAMSA/libs/libdeflate/Makefile
vendor/FAMSA/libs/libdeflate/NEWS.md
vendor/FAMSA/libs/libdeflate/README.md
vendor/FAMSA/libs/libdeflate/libdeflate.h
vendor/FAMSA/libs/libdeflate/common/common_defs.h
vendor/FAMSA/libs/libdeflate/common/compiler_gcc.h
vendor/FAMSA/libs/libdeflate/common/compiler_msc.h
vendor/FAMSA/libs/libdeflate/lib/adler32.c
vendor/FAMSA/libs/libdeflate/lib/adler32_vec_template.h
vendor/FAMSA/libs/libdeflate/lib/bt_matchfinder.h
vendor/FAMSA/libs/libdeflate/lib/cpu_features_common.h
vendor/FAMSA/libs/libdeflate/lib/crc32.c
vendor/FAMSA/libs/libdeflate/lib/crc32_table.h
vendor/FAMSA/libs/libdeflate/lib/crc32_vec_template.h
vendor/FAMSA/libs/libdeflate/lib/decompress_template.h
vendor/FAMSA/libs/libdeflate/lib/deflate_compress.c
vendor/FAMSA/libs/libdeflate/lib/deflate_compress.h
vendor/FAMSA/libs/libdeflate/lib/deflate_constants.h
vendor/FAMSA/libs/libdeflate/lib/deflate_decompress.c
vendor/FAMSA/libs/libdeflate/lib/gzip_compress.c
vendor/FAMSA/libs/libdeflate/lib/gzip_constants.h
vendor/FAMSA/libs/libdeflate/lib/gzip_decompress.c
vendor/FAMSA/libs/libdeflate/lib/hc_matchfinder.h
vendor/FAMSA/libs/libdeflate/lib/ht_matchfinder.h
vendor/FAMSA/libs/libdeflate/lib/lib_common.h
vendor/FAMSA/libs/libdeflate/lib/matchfinder_common.h
vendor/FAMSA/libs/libdeflate/lib/unaligned.h
vendor/FAMSA/libs/libdeflate/lib/utils.c
vendor/FAMSA/libs/libdeflate/lib/zlib_compress.c
vendor/FAMSA/libs/libdeflate/lib/zlib_constants.h
vendor/FAMSA/libs/libdeflate/lib/zlib_decompress.c
vendor/FAMSA/libs/libdeflate/lib/arm/adler32_impl.h
vendor/FAMSA/libs/libdeflate/lib/arm/cpu_features.c
vendor/FAMSA/libs/libdeflate/lib/arm/cpu_features.h
vendor/FAMSA/libs/libdeflate/lib/arm/crc32_impl.h
vendor/FAMSA/libs/libdeflate/lib/arm/matchfinder_impl.h
vendor/FAMSA/libs/libdeflate/lib/x86/adler32_impl.h
vendor/FAMSA/libs/libdeflate/lib/x86/cpu_features.c
vendor/FAMSA/libs/libdeflate/lib/x86/cpu_features.h
vendor/FAMSA/libs/libdeflate/lib/x86/crc32_impl.h
vendor/FAMSA/libs/libdeflate/lib/x86/crc32_pclmul_template.h
vendor/FAMSA/libs/libdeflate/lib/x86/decompress_impl.h
vendor/FAMSA/libs/libdeflate/lib/x86/matchfinder_impl.h
vendor/FAMSA/libs/libdeflate/programs/benchmark.c
vendor/FAMSA/libs/libdeflate/programs/checksum.c
vendor/FAMSA/libs/libdeflate/programs/gzip.c
vendor/FAMSA/libs/libdeflate/programs/prog_util.c
vendor/FAMSA/libs/libdeflate/programs/prog_util.h
vendor/FAMSA/libs/libdeflate/programs/test_checksums.c
vendor/FAMSA/libs/libdeflate/programs/test_custom_malloc.c
vendor/FAMSA/libs/libdeflate/programs/test_incomplete_codes.c
vendor/FAMSA/libs/libdeflate/programs/test_litrunlen_overflow.c
vendor/FAMSA/libs/libdeflate/programs/test_overread.c
vendor/FAMSA/libs/libdeflate/programs/test_slow_decompression.c
vendor/FAMSA/libs/libdeflate/programs/test_trailing_bytes.c
vendor/FAMSA/libs/libdeflate/programs/test_util.c
vendor/FAMSA/libs/libdeflate/programs/test_util.h
vendor/FAMSA/libs/libdeflate/programs/tgetopt.c
vendor/FAMSA/libs/libdeflate/scripts/detect.sh
vendor/FAMSA/libs/libdeflate/windows/libdeflatestatic.lib
vendor/FAMSA/libs/mimalloc/alloc-aligned.c
vendor/FAMSA/libs/mimalloc/alloc-override-osx.c
vendor/FAMSA/libs/mimalloc/alloc-override.c
vendor/FAMSA/libs/mimalloc/alloc-posix.c
vendor/FAMSA/libs/mimalloc/alloc.c
vendor/FAMSA/libs/mimalloc/arena.c
vendor/FAMSA/libs/mimalloc/bitmap.c
vendor/FAMSA/libs/mimalloc/bitmap.h
vendor/FAMSA/libs/mimalloc/heap.c
vendor/FAMSA/libs/mimalloc/init.c
vendor/FAMSA/libs/mimalloc/mimalloc-LICENSE
vendor/FAMSA/libs/mimalloc/mimalloc-atomic.h
vendor/FAMSA/libs/mimalloc/mimalloc-internal.h
vendor/FAMSA/libs/mimalloc/mimalloc-new-delete.h
vendor/FAMSA/libs/mimalloc/mimalloc-override.h
vendor/FAMSA/libs/mimalloc/mimalloc-types.h
vendor/FAMSA/libs/mimalloc/mimalloc.h
vendor/FAMSA/libs/mimalloc/options.c
vendor/FAMSA/libs/mimalloc/os.c
vendor/FAMSA/libs/mimalloc/override-new-delete.cpp
vendor/FAMSA/libs/mimalloc/page-queue.c
vendor/FAMSA/libs/mimalloc/page.c
vendor/FAMSA/libs/mimalloc/random.c
vendor/FAMSA/libs/mimalloc/region.c
vendor/FAMSA/libs/mimalloc/segment-cache.c
vendor/FAMSA/libs/mimalloc/segment.c
vendor/FAMSA/libs/mimalloc/static.cpp
vendor/FAMSA/libs/mimalloc/stats.c
vendor/FAMSA/src/famsa.cpp
vendor/FAMSA/src/msa.cpp
vendor/FAMSA/src/msa.h
vendor/FAMSA/src/msa_refinement.cpp
vendor/FAMSA/src/core/defs.h
vendor/FAMSA/src/core/io_service.cpp
vendor/FAMSA/src/core/io_service.h
vendor/FAMSA/src/core/params.cpp
vendor/FAMSA/src/core/params.h
vendor/FAMSA/src/core/profile.cpp
vendor/FAMSA/src/core/profile.h
vendor/FAMSA/src/core/profile_par.cpp
vendor/FAMSA/src/core/profile_seq.cpp
vendor/FAMSA/src/core/queues.cpp
vendor/FAMSA/src/core/queues.h
vendor/FAMSA/src/core/sequence.cpp
vendor/FAMSA/src/core/sequence.h
vendor/FAMSA/src/core/version.h
vendor/FAMSA/src/lcs/lcsbp.cpp
vendor/FAMSA/src/lcs/lcsbp.h
vendor/FAMSA/src/lcs/lcsbp_avx2_intr.cpp
vendor/FAMSA/src/lcs/lcsbp_avx2_intr.h
vendor/FAMSA/src/lcs/lcsbp_avx_intr.cpp
vendor/FAMSA/src/lcs/lcsbp_avx_intr.h
vendor/FAMSA/src/lcs/lcsbp_classic.cpp
vendor/FAMSA/src/lcs/lcsbp_classic.h
vendor/FAMSA/src/lcs/lcsbp_neon_intr.cpp
vendor/FAMSA/src/lcs/lcsbp_neon_intr.h
vendor/FAMSA/src/tree/AbstractTreeGenerator.cpp
vendor/FAMSA/src/tree/AbstractTreeGenerator.h
vendor/FAMSA/src/tree/AbstractTreeGenerator.hpp
vendor/FAMSA/src/tree/Chained.h
vendor/FAMSA/src/tree/Clustering.cpp
vendor/FAMSA/src/tree/Clustering.h
vendor/FAMSA/src/tree/DistanceCalculator.cpp
vendor/FAMSA/src/tree/DistanceCalculator.h
vendor/FAMSA/src/tree/FastTree.cpp
vendor/FAMSA/src/tree/FastTree.h
vendor/FAMSA/src/tree/GuideTree.cpp
vendor/FAMSA/src/tree/GuideTree.h
vendor/FAMSA/src/tree/IPartialGenerator.h
vendor/FAMSA/src/tree/MSTPrim.cpp
vendor/FAMSA/src/tree/MSTPrim.h
vendor/FAMSA/src/tree/NeighborJoining.cpp
vendor/FAMSA/src/tree/NeighborJoining.h
vendor/FAMSA/src/tree/NewickParser.cpp
vendor/FAMSA/src/tree/NewickParser.h
vendor/FAMSA/src/tree/SingleLinkage.cpp
vendor/FAMSA/src/tree/SingleLinkage.h
vendor/FAMSA/src/tree/SingleLinkageQueue.h
vendor/FAMSA/src/tree/TreeDefs.h
vendor/FAMSA/src/tree/UPGMA.cpp
vendor/FAMSA/src/tree/UPGMA.h
vendor/FAMSA/src/utils/array.h
vendor/FAMSA/src/utils/conversion.h
vendor/FAMSA/src/utils/cpuid.h
vendor/FAMSA/src/utils/deterministic_random.h
vendor/FAMSA/src/utils/log.cpp
vendor/FAMSA/src/utils/log.h
vendor/FAMSA/src/utils/memory_monotonic.h
vendor/FAMSA/src/utils/meta_oper.h
vendor/FAMSA/src/utils/pooled_threads.cpp
vendor/FAMSA/src/utils/pooled_threads.h
vendor/FAMSA/src/utils/statistics.h
vendor/FAMSA/src/utils/timer.cpp
vendor/FAMSA/src/utils/timer.h
vendor/FAMSA/src/utils/utils.cpp
vendor/FAMSA/src/utils/utils.h
vendor/FAMSA/src/utils/utils_avx.cpp
vendor/FAMSA/src/utils/utils_avx2.cpp
vendor/FAMSA/src/utils/utils_neon.cpp