CHANGELOG.md
CONTRIBUTING.md
COPYING
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
include/_unicode.pxd
include/iostream.pxd
include/cpu_features/__init__.pxd
include/cpu_features/aarch64.pxd
include/cpu_features/arm.pxd
include/cpu_features/x86.pxd
include/trimal/__init__.pxd
include/trimal/alignment.pxd
include/trimal/cleaner.pxd
include/trimal/format_handling.pxd
include/trimal/manager.pxd
include/trimal/report_system.pxd
include/trimal/sequences_matrix.pxd
include/trimal/similarity_matrix.pxd
include/trimal/statistics.pxd
patches/BaseFormatHandler.h.patch
patches/Cleaner.cpp.patch
patches/Cleaner.h.patch
patches/Gaps.h.patch
patches/Similarity.h.patch
patches/clustal_state.cpp.patch
patches/clustal_state.h.patch
patches/fasta_m10_state.cpp.patch
patches/fasta_m10_state.h.patch
patches/fasta_state.cpp.patch
patches/fasta_state.h.patch
patches/htmlreport_state.cpp.patch
patches/htmlreport_state.h.patch
patches/mega_interleaved_state.cpp.patch
patches/mega_interleaved_state.h.patch
patches/mega_sequential_state.cpp.patch
patches/mega_sequential_state.h.patch
patches/nexus_m10_state.cpp.patch
patches/nexus_m10_state.h.patch
patches/nexus_state.cpp.patch
patches/nexus_state.h.patch
patches/phylip32_m10_state.cpp.patch
patches/phylip32_m10_state.h.patch
patches/phylip32_state.cpp.patch
patches/phylip32_state.h.patch
patches/phylip40_m10_state.cpp.patch
patches/phylip40_m10_state.h.patch
patches/phylip40_state.cpp.patch
patches/phylip40_state.h.patch
patches/phylip_paml_m10_state.cpp.patch
patches/phylip_paml_m10_state.h.patch
patches/phylip_paml_state.cpp.patch
patches/phylip_paml_state.h.patch
patches/pir_state.cpp.patch
patches/pir_state.h.patch
patches/similarityMatrix.h.patch
patches/trimalManager.h.patch
pytrimal/__init__.py
pytrimal/_trimal.pxd
pytrimal/_trimal.pyi
pytrimal/_trimal.pyx
pytrimal/_version.py
pytrimal/py.typed
pytrimal.egg-info/PKG-INFO
pytrimal.egg-info/SOURCES.txt
pytrimal.egg-info/dependency_links.txt
pytrimal.egg-info/not-zip-safe
pytrimal.egg-info/top_level.txt
pytrimal/fileobj/__init__.pxd
pytrimal/fileobj/pyreadbuf.cpp
pytrimal/fileobj/pyreadbuf.h
pytrimal/fileobj/pyreadintobuf.cpp
pytrimal/fileobj/pyreadintobuf.h
pytrimal/fileobj/pywritebuf.cpp
pytrimal/fileobj/pywritebuf.h
pytrimal/impl/__init__.pxd
pytrimal/impl/avx.cpp
pytrimal/impl/avx.h
pytrimal/impl/avx.pxd
pytrimal/impl/generic.cpp
pytrimal/impl/generic.h
pytrimal/impl/generic.pxd
pytrimal/impl/mmx.cpp
pytrimal/impl/mmx.h
pytrimal/impl/mmx.pxd
pytrimal/impl/neon.cpp
pytrimal/impl/neon.h
pytrimal/impl/neon.pxd
pytrimal/impl/sse.cpp
pytrimal/impl/sse.h
pytrimal/impl/sse.pxd
pytrimal/impl/template.h
pytrimal/patch/omp.h
pytrimal/patch/reportsystem.cpp
pytrimal/tests/__init__.py
pytrimal/tests/__main__.py
pytrimal/tests/requirements.txt
pytrimal/tests/test_alignment.py
pytrimal/tests/test_automatic_trimmer.py
pytrimal/tests/test_doctest.py
pytrimal/tests/test_manual_trimmer.py
pytrimal/tests/test_overlap_trimmer.py
pytrimal/tests/test_representative_trimmer.py
pytrimal/tests/test_similarity_matrix.py
pytrimal/tests/data/ENOG411BWBU.automated1.fasta
pytrimal/tests/data/ENOG411BWBU.clusters10.fasta
pytrimal/tests/data/ENOG411BWBU.clusters5.fasta
pytrimal/tests/data/ENOG411BWBU.cons40.gt40.fasta
pytrimal/tests/data/ENOG411BWBU.cons60.gt90.fasta
pytrimal/tests/data/ENOG411BWBU.fasta
pytrimal/tests/data/ENOG411BWBU.gappyout.fasta
pytrimal/tests/data/ENOG411BWBU.id50.fasta
pytrimal/tests/data/ENOG411BWBU.id70.fasta
pytrimal/tests/data/ENOG411BWBU.maxidentity75.fasta
pytrimal/tests/data/ENOG411BWBU.noallgaps.fasta
pytrimal/tests/data/ENOG411BWBU.noduplicateseqs.fasta
pytrimal/tests/data/ENOG411BWBU.seq40.res60.fasta
pytrimal/tests/data/ENOG411BWBU.seq80.res80.fasta
pytrimal/tests/data/ENOG411BWBU.strict.fasta
pytrimal/tests/data/ENOG411BWBU.strictplus.fasta
pytrimal/tests/data/PF12574.full.afa
pytrimal/tests/data/__init__.py
pytrimal/tests/data/example.001.AA.clw
pytrimal/tests/data/example.001.gt90.w3.fasta
pytrimal/tests/data/halorhodopsin.afa
pytrimal/tests/data/pam70.json
vendor/cpu_features/CONTRIBUTING.md
vendor/cpu_features/LICENSE
vendor/cpu_features/README.md
vendor/cpu_features/ci/README.md
vendor/cpu_features/cmake/README.md
vendor/cpu_features/include/cpu_features_cache_info.h
vendor/cpu_features/include/cpu_features_macros.h
vendor/cpu_features/include/cpuinfo_aarch64.h
vendor/cpu_features/include/cpuinfo_arm.h
vendor/cpu_features/include/cpuinfo_mips.h
vendor/cpu_features/include/cpuinfo_ppc.h
vendor/cpu_features/include/cpuinfo_x86.h
vendor/cpu_features/include/internal/bit_utils.h
vendor/cpu_features/include/internal/cpuid_x86.h
vendor/cpu_features/include/internal/filesystem.h
vendor/cpu_features/include/internal/hwcaps.h
vendor/cpu_features/include/internal/stack_line_reader.h
vendor/cpu_features/include/internal/string_view.h
vendor/cpu_features/ndk_compat/README.md
vendor/cpu_features/src/copy.inl
vendor/cpu_features/src/define_introspection.inl
vendor/cpu_features/src/define_introspection_and_hwcaps.inl
vendor/cpu_features/src/equals.inl
vendor/cpu_features/src/filesystem.c
vendor/cpu_features/src/hwcaps.c
vendor/cpu_features/src/impl_aarch64_linux_or_android.c
vendor/cpu_features/src/impl_arm_linux_or_android.c
vendor/cpu_features/src/impl_mips_linux_or_android.c
vendor/cpu_features/src/impl_ppc_linux.c
vendor/cpu_features/src/impl_x86__base_implementation.inl
vendor/cpu_features/src/impl_x86_freebsd.c
vendor/cpu_features/src/impl_x86_linux_or_android.c
vendor/cpu_features/src/impl_x86_macos.c
vendor/cpu_features/src/impl_x86_windows.c
vendor/cpu_features/src/stack_line_reader.c
vendor/cpu_features/src/string_view.c
vendor/cpu_features/src/utils/list_cpu_features.c
vendor/trimal/AUTHORS
vendor/trimal/CHANGELOG
vendor/trimal/CMakeLists.txt
vendor/trimal/LICENSE
vendor/trimal/README.md
vendor/trimal/dataset/alignments_comparison.1
vendor/trimal/dataset/alignments_comparison.2
vendor/trimal/dataset/alignments_comparison.3
vendor/trimal/dataset/example.001.AA.clw
vendor/trimal/dataset/example.001.AA.msl
vendor/trimal/dataset/example.001.AA.phy
vendor/trimal/dataset/example.002.AA.clw
vendor/trimal/dataset/example.002.AA.phy
vendor/trimal/dataset/example.003.AA.clw
vendor/trimal/dataset/example.004.AA.fasta
vendor/trimal/dataset/example.005.AA.fasta
vendor/trimal/dataset/example.006.AA.pir
vendor/trimal/dataset/example.007.AA.fasta
vendor/trimal/dataset/example.007.AA.only_seqs
vendor/trimal/dataset/example.009.AA.fasta
vendor/trimal/dataset/example.010.AA.fasta
vendor/trimal/dataset/example.011.AA.YKL197C.clw
vendor/trimal/dataset/example.011.AA.YKL197C.fasta
vendor/trimal/dataset/example.011.AA.YKL197C.phy
vendor/trimal/dataset/example.012.AA.SuperAlignment.phy
vendor/trimal/dataset/example.013.AA.SuperAlignment.phy
vendor/trimal/dataset/example.014.AA.EggNOG.COG0591.fasta
vendor/trimal/dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta
vendor/trimal/dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta
vendor/trimal/dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta
vendor/trimal/dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta
vendor/trimal/dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta
vendor/trimal/dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta
vendor/trimal/dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta
vendor/trimal/dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta
vendor/trimal/dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta
vendor/trimal/dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta
vendor/trimal/dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta
vendor/trimal/dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta
vendor/trimal/dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta
vendor/trimal/dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta
vendor/trimal/dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta
vendor/trimal/dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta
vendor/trimal/dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta
vendor/trimal/dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta
vendor/trimal/dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta
vendor/trimal/dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta
vendor/trimal/dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta
vendor/trimal/dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta
vendor/trimal/dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta
vendor/trimal/dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta
vendor/trimal/dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta
vendor/trimal/dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta
vendor/trimal/dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta
vendor/trimal/dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta
vendor/trimal/dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta
vendor/trimal/dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta
vendor/trimal/dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta
vendor/trimal/dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta
vendor/trimal/dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta
vendor/trimal/dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta
vendor/trimal/dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta
vendor/trimal/dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta
vendor/trimal/dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta
vendor/trimal/dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta
vendor/trimal/dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta
vendor/trimal/dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta
vendor/trimal/dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta
vendor/trimal/dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta
vendor/trimal/dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta
vendor/trimal/dataset/example.058.AA.strNOG.ENOG411BBR6.fasta
vendor/trimal/dataset/example.059.AA.strNOG.ENOG411BBRR.fasta
vendor/trimal/dataset/example.060.AA.strNOG.ENOG411BBWK.fasta
vendor/trimal/dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta
vendor/trimal/dataset/example.062.AA.strNOG.ENOG411BCX3.fasta
vendor/trimal/dataset/example.063.AA.strNOG.ENOG411BDBU.fasta
vendor/trimal/dataset/example.064.AA.strNOG.ENOG411BDKC.fasta
vendor/trimal/dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta
vendor/trimal/dataset/example.066.AA.strNOG.ENOG411BDUE.fasta
vendor/trimal/dataset/example.067.AA.strNOG.ENOG411BDX3.fasta
vendor/trimal/dataset/example.068.AA.strNOG.ENOG411BE45.fasta
vendor/trimal/dataset/example.069.AA.strNOG.ENOG411BE8B.fasta
vendor/trimal/dataset/example.070.AA.strNOG.ENOG411BEUV.fasta
vendor/trimal/dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta
vendor/trimal/dataset/example.072.AA.strNOG.ENOG411BF1S.fasta
vendor/trimal/dataset/example.073.AA.strNOG.ENOG411BFCW.fasta
vendor/trimal/dataset/example.074.AA.strNOG.ENOG411BFPF.fasta
vendor/trimal/dataset/example.075.AA.strNOG.ENOG411BFQS.fasta
vendor/trimal/dataset/example.076.AA.strNOG.ENOG411BH75.fasta
vendor/trimal/dataset/example.077.AA.strNOG.ENOG411BH79.fasta
vendor/trimal/dataset/example.078.AA.strNOG.ENOG411BH99.fasta
vendor/trimal/dataset/example.079.AA.strNOG.ENOG411BJDC.fasta
vendor/trimal/dataset/example.080.AA.strNOG.ENOG411BJIF.fasta
vendor/trimal/dataset/example.081.AA.strNOG.ENOG411BK9X.fasta
vendor/trimal/dataset/example.082.AA.strNOG.ENOG411BKC5.fasta
vendor/trimal/dataset/example.083.AA.strNOG.ENOG411BMKC.fasta
vendor/trimal/dataset/example.084.AA.strNOG.ENOG411BNP9.fasta
vendor/trimal/dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta
vendor/trimal/dataset/example.086.AA.strNOG.ENOG411BR1D.fasta
vendor/trimal/dataset/example.087.AA.strNOG.ENOG411BRCH.fasta
vendor/trimal/dataset/example.088.AA.strNOG.ENOG411BSXF.fasta
vendor/trimal/dataset/example.089.AA.strNOG.ENOG411BV9B.fasta
vendor/trimal/dataset/example.090.AA.strNOG.ENOG411BVKR.fasta
vendor/trimal/dataset/example.091.AA.strNOG.ENOG411BWBU.codon.fa
vendor/trimal/dataset/example.091.AA.strNOG.ENOG411BWBU.fasta
vendor/trimal/dataset/example.092.DNA.fasta
vendor/trimal/dataset/example.093.DNA.fasta
vendor/trimal/dataset/example.094.DNADeg.sequential_phy
vendor/trimal/dataset/matrix.BLOSUM62
vendor/trimal/dataset/matrix.Degenerated_DNA
vendor/trimal/include/Cleaner.h
vendor/trimal/include/InternalBenchmarker.h
vendor/trimal/include/VCFHandler.h
vendor/trimal/include/defines.h
vendor/trimal/include/reportsystem.h
vendor/trimal/include/trimalManager.h
vendor/trimal/include/utils.h
vendor/trimal/include/values.h
vendor/trimal/include/Alignment/Alignment.h
vendor/trimal/include/Alignment/sequencesMatrix.h
vendor/trimal/include/FormatHandling/BaseFormatHandler.h
vendor/trimal/include/FormatHandling/FormatManager.h
vendor/trimal/include/FormatHandling/clustal_state.h
vendor/trimal/include/FormatHandling/fasta_m10_state.h
vendor/trimal/include/FormatHandling/fasta_state.h
vendor/trimal/include/FormatHandling/formats_header.h
vendor/trimal/include/FormatHandling/htmlreport_state.h
vendor/trimal/include/FormatHandling/mega_interleaved_state.h
vendor/trimal/include/FormatHandling/mega_sequential_state.h
vendor/trimal/include/FormatHandling/nexus_m10_state.h
vendor/trimal/include/FormatHandling/nexus_state.h
vendor/trimal/include/FormatHandling/phylip32_m10_state.h
vendor/trimal/include/FormatHandling/phylip32_state.h
vendor/trimal/include/FormatHandling/phylip40_m10_state.h
vendor/trimal/include/FormatHandling/phylip40_state.h
vendor/trimal/include/FormatHandling/phylip_paml_m10_state.h
vendor/trimal/include/FormatHandling/phylip_paml_state.h
vendor/trimal/include/FormatHandling/pir_state.h
vendor/trimal/include/RawText/examples.txt
vendor/trimal/include/RawText/legacyMenu.txt
vendor/trimal/include/RawText/menu.txt
vendor/trimal/include/Statistics/Consistency.h
vendor/trimal/include/Statistics/Gaps.h
vendor/trimal/include/Statistics/Manager.h
vendor/trimal/include/Statistics/Mold.h
vendor/trimal/include/Statistics/Similarity.h
vendor/trimal/include/Statistics/similarityMatrix.h
vendor/trimal/source/Cleaner.cpp
vendor/trimal/source/InternalBenchmarker.cpp
vendor/trimal/source/VCFHandler.cpp
vendor/trimal/source/alignment.cpp
vendor/trimal/source/compareFiles.cpp
vendor/trimal/source/main.cpp
vendor/trimal/source/reportsystem.cpp
vendor/trimal/source/rwAlignment.cpp
vendor/trimal/source/trimAlMain.cpp
vendor/trimal/source/trimalManager.cpp
vendor/trimal/source/typeHelper.cpp
vendor/trimal/source/utils.cpp
vendor/trimal/source/Alignment/Alignment.cpp
vendor/trimal/source/Alignment/sequencesMatrix.cpp
vendor/trimal/source/FormatHandling/BaseFormatHandler.cpp
vendor/trimal/source/FormatHandling/clustal_state.cpp
vendor/trimal/source/FormatHandling/fasta_m10_state.cpp
vendor/trimal/source/FormatHandling/fasta_state.cpp
vendor/trimal/source/FormatHandling/htmlreport_state.cpp
vendor/trimal/source/FormatHandling/mega_interleaved_state.cpp
vendor/trimal/source/FormatHandling/mega_sequential_state.cpp
vendor/trimal/source/FormatHandling/nexus_m10_state.cpp
vendor/trimal/source/FormatHandling/nexus_state.cpp
vendor/trimal/source/FormatHandling/phylip32_m10_state.cpp
vendor/trimal/source/FormatHandling/phylip32_state.cpp
vendor/trimal/source/FormatHandling/phylip40_m10_state.cpp
vendor/trimal/source/FormatHandling/phylip40_state.cpp
vendor/trimal/source/FormatHandling/phylip_paml_m10_state.cpp
vendor/trimal/source/FormatHandling/phylip_paml_state.cpp
vendor/trimal/source/FormatHandling/pir_state.cpp
vendor/trimal/source/FormatHandling/readAlMain.cpp
vendor/trimal/source/Statistics/Consistency.cpp
vendor/trimal/source/Statistics/Gaps.cpp
vendor/trimal/source/Statistics/Manager.cpp
vendor/trimal/source/Statistics/Mold.cpp
vendor/trimal/source/Statistics/Similarity.cpp
vendor/trimal/source/Statistics/similarityMatrix.cpp
vendor/trimal/source/reportMessages/errorMessages.cpp
vendor/trimal/source/reportMessages/infoMessages.cpp
vendor/trimal/source/reportMessages/warningMessages.cpp