CHANGELOG.md
CONTRIBUTING.md
COPYING
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
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/Cleaner.cpp.patch
patches/Manager.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/requires.txt
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/patch/omp.h
pytrimal/patch/reportsystem.cpp
pytrimal/tests/__init__.py
pytrimal/tests/__main__.py
pytrimal/tests/_base.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.clw
pytrimal/tests/data/halorhodopsin.afa
pytrimal/tests/data/pam70.json
vendor/trimal/AUTHORS
vendor/trimal/CHANGELOG
vendor/trimal/CMakeLists.txt
vendor/trimal/LICENSE
vendor/trimal/README.md
vendor/trimal/dataset/example.001.AA.clw
vendor/trimal/dataset/example.091.AA.strNOG.ENOG411BWBU.fasta
vendor/trimal/dataset/trimmed_msas/automated1/example.091.AA.strNOG.ENOG411BWBU.fasta
vendor/trimal/dataset/trimmed_msas/gappyout/example.091.AA.strNOG.ENOG411BWBU.fasta
vendor/trimal/dataset/trimmed_msas/noallgaps/example.091.AA.strNOG.ENOG411BWBU.fasta
vendor/trimal/dataset/trimmed_msas/nogaps/example.091.AA.strNOG.ENOG411BWBU.fasta
vendor/trimal/dataset/trimmed_msas/strict/example.091.AA.strNOG.ENOG411BWBU.fasta
vendor/trimal/dataset/trimmed_msas/strictplus/example.091.AA.strNOG.ENOG411BWBU.fasta
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/residueValues.h
vendor/trimal/include/trimalManager.h
vendor/trimal/include/utils.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/Platform/template.h
vendor/trimal/include/Platform/Arm/NEON.h
vendor/trimal/include/Platform/x86/AVX2.h
vendor/trimal/include/Platform/x86/SSE2.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/Identity.h
vendor/trimal/include/Statistics/Manager.h
vendor/trimal/include/Statistics/Mold.h
vendor/trimal/include/Statistics/Overlap.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/reportsystem.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/Platform/Arm/NEON.cpp
vendor/trimal/source/Platform/x86/AVX2.cpp
vendor/trimal/source/Platform/x86/SSE2.cpp
vendor/trimal/source/Statistics/Consistency.cpp
vendor/trimal/source/Statistics/Gaps.cpp
vendor/trimal/source/Statistics/Identity.cpp
vendor/trimal/source/Statistics/Manager.cpp
vendor/trimal/source/Statistics/Mold.cpp
vendor/trimal/source/Statistics/Overlap.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
vendor/trimal/vendor/cpu_features/.clang-format
vendor/trimal/vendor/cpu_features/.dockerignore
vendor/trimal/vendor/cpu_features/.git
vendor/trimal/vendor/cpu_features/.gitignore
vendor/trimal/vendor/cpu_features/.grenrc.yml
vendor/trimal/vendor/cpu_features/BUILD.bazel
vendor/trimal/vendor/cpu_features/CMakeLists.txt
vendor/trimal/vendor/cpu_features/CONTRIBUTING.md
vendor/trimal/vendor/cpu_features/LICENSE
vendor/trimal/vendor/cpu_features/README.md
vendor/trimal/vendor/cpu_features/WORKSPACE
vendor/trimal/vendor/cpu_features/.github/workflows/Dockerfile
vendor/trimal/vendor/cpu_features/.github/workflows/aarch64_linux_bazel.yml
vendor/trimal/vendor/cpu_features/.github/workflows/aarch64_linux_cmake.yml
vendor/trimal/vendor/cpu_features/.github/workflows/amd64_freebsd_cmake.yml
vendor/trimal/vendor/cpu_features/.github/workflows/amd64_linux_bazel.yml
vendor/trimal/vendor/cpu_features/.github/workflows/amd64_linux_cmake.yml
vendor/trimal/vendor/cpu_features/.github/workflows/amd64_macos_bazel.yml
vendor/trimal/vendor/cpu_features/.github/workflows/amd64_macos_cmake.yml
vendor/trimal/vendor/cpu_features/.github/workflows/amd64_windows_cmake.yml
vendor/trimal/vendor/cpu_features/.github/workflows/arm_linux_cmake.yml
vendor/trimal/vendor/cpu_features/.github/workflows/clang_format.yml
vendor/trimal/vendor/cpu_features/.github/workflows/mips_linux_cmake.yml
vendor/trimal/vendor/cpu_features/.github/workflows/power_linux_cmake.yml
vendor/trimal/vendor/cpu_features/.github/workflows/riscv_linux_cmake.yml
vendor/trimal/vendor/cpu_features/.github/workflows/s390x_linux_cmake.yml
vendor/trimal/vendor/cpu_features/bazel/platforms.bzl
vendor/trimal/vendor/cpu_features/bazel/ci/Makefile
vendor/trimal/vendor/cpu_features/bazel/ci/README.md
vendor/trimal/vendor/cpu_features/bazel/ci/docker/Dockerfile
vendor/trimal/vendor/cpu_features/cmake/CpuFeaturesConfig.cmake.in
vendor/trimal/vendor/cpu_features/cmake/CpuFeaturesNdkCompatConfig.cmake.in
vendor/trimal/vendor/cpu_features/cmake/README.md
vendor/trimal/vendor/cpu_features/cmake/googletest.CMakeLists.txt.in
vendor/trimal/vendor/cpu_features/cmake/ci/Makefile
vendor/trimal/vendor/cpu_features/cmake/ci/README.md
vendor/trimal/vendor/cpu_features/cmake/ci/doc/docker.dot
vendor/trimal/vendor/cpu_features/cmake/ci/doc/docker.svg
vendor/trimal/vendor/cpu_features/cmake/ci/doc/generate_image.sh
vendor/trimal/vendor/cpu_features/cmake/ci/docker/amd64/Dockerfile
vendor/trimal/vendor/cpu_features/cmake/ci/docker/toolchain/Dockerfile
vendor/trimal/vendor/cpu_features/cmake/ci/sample/CMakeLists.txt
vendor/trimal/vendor/cpu_features/cmake/ci/sample/main.cpp
vendor/trimal/vendor/cpu_features/cmake/ci/vagrant/freebsd/Vagrantfile
vendor/trimal/vendor/cpu_features/include/cpu_features_cache_info.h
vendor/trimal/vendor/cpu_features/include/cpu_features_macros.h
vendor/trimal/vendor/cpu_features/include/cpuinfo_aarch64.h
vendor/trimal/vendor/cpu_features/include/cpuinfo_arm.h
vendor/trimal/vendor/cpu_features/include/cpuinfo_loongarch.h
vendor/trimal/vendor/cpu_features/include/cpuinfo_mips.h
vendor/trimal/vendor/cpu_features/include/cpuinfo_ppc.h
vendor/trimal/vendor/cpu_features/include/cpuinfo_riscv.h
vendor/trimal/vendor/cpu_features/include/cpuinfo_s390x.h
vendor/trimal/vendor/cpu_features/include/cpuinfo_x86.h
vendor/trimal/vendor/cpu_features/include/internal/bit_utils.h
vendor/trimal/vendor/cpu_features/include/internal/cpuid_x86.h
vendor/trimal/vendor/cpu_features/include/internal/filesystem.h
vendor/trimal/vendor/cpu_features/include/internal/hwcaps.h
vendor/trimal/vendor/cpu_features/include/internal/stack_line_reader.h
vendor/trimal/vendor/cpu_features/include/internal/string_view.h
vendor/trimal/vendor/cpu_features/include/internal/windows_utils.h
vendor/trimal/vendor/cpu_features/ndk_compat/CMakeLists.txt
vendor/trimal/vendor/cpu_features/ndk_compat/README.md
vendor/trimal/vendor/cpu_features/ndk_compat/cpu-features.c
vendor/trimal/vendor/cpu_features/ndk_compat/cpu-features.h
vendor/trimal/vendor/cpu_features/ndk_compat/ndk-compat-test.c
vendor/trimal/vendor/cpu_features/scripts/generate_badges.d
vendor/trimal/vendor/cpu_features/scripts/make_release.sh
vendor/trimal/vendor/cpu_features/scripts/run_integration.sh
vendor/trimal/vendor/cpu_features/scripts/test_integration.sh
vendor/trimal/vendor/cpu_features/src/copy.inl
vendor/trimal/vendor/cpu_features/src/define_introspection.inl
vendor/trimal/vendor/cpu_features/src/define_introspection_and_hwcaps.inl
vendor/trimal/vendor/cpu_features/src/equals.inl
vendor/trimal/vendor/cpu_features/src/filesystem.c
vendor/trimal/vendor/cpu_features/src/hwcaps.c
vendor/trimal/vendor/cpu_features/src/impl_aarch64__base_implementation.inl
vendor/trimal/vendor/cpu_features/src/impl_aarch64_linux_or_android.c
vendor/trimal/vendor/cpu_features/src/impl_aarch64_macos_or_iphone.c
vendor/trimal/vendor/cpu_features/src/impl_aarch64_windows.c
vendor/trimal/vendor/cpu_features/src/impl_arm_linux_or_android.c
vendor/trimal/vendor/cpu_features/src/impl_loongarch_linux.c
vendor/trimal/vendor/cpu_features/src/impl_mips_linux_or_android.c
vendor/trimal/vendor/cpu_features/src/impl_ppc_linux.c
vendor/trimal/vendor/cpu_features/src/impl_riscv_linux.c
vendor/trimal/vendor/cpu_features/src/impl_s390x_linux.c
vendor/trimal/vendor/cpu_features/src/impl_x86__base_implementation.inl
vendor/trimal/vendor/cpu_features/src/impl_x86_freebsd.c
vendor/trimal/vendor/cpu_features/src/impl_x86_linux_or_android.c
vendor/trimal/vendor/cpu_features/src/impl_x86_macos.c
vendor/trimal/vendor/cpu_features/src/impl_x86_windows.c
vendor/trimal/vendor/cpu_features/src/stack_line_reader.c
vendor/trimal/vendor/cpu_features/src/string_view.c
vendor/trimal/vendor/cpu_features/src/utils/list_cpu_features.c
vendor/trimal/vendor/cpu_features/test/CMakeLists.txt
vendor/trimal/vendor/cpu_features/test/bit_utils_test.cc
vendor/trimal/vendor/cpu_features/test/cpuinfo_aarch64_test.cc
vendor/trimal/vendor/cpu_features/test/cpuinfo_arm_test.cc
vendor/trimal/vendor/cpu_features/test/cpuinfo_loongarch_test.cc
vendor/trimal/vendor/cpu_features/test/cpuinfo_mips_test.cc
vendor/trimal/vendor/cpu_features/test/cpuinfo_ppc_test.cc
vendor/trimal/vendor/cpu_features/test/cpuinfo_riscv_test.cc
vendor/trimal/vendor/cpu_features/test/cpuinfo_s390x_test.cc
vendor/trimal/vendor/cpu_features/test/cpuinfo_x86_test.cc
vendor/trimal/vendor/cpu_features/test/filesystem_for_testing.cc
vendor/trimal/vendor/cpu_features/test/filesystem_for_testing.h
vendor/trimal/vendor/cpu_features/test/hwcaps_for_testing.cc
vendor/trimal/vendor/cpu_features/test/hwcaps_for_testing.h
vendor/trimal/vendor/cpu_features/test/stack_line_reader_test.cc
vendor/trimal/vendor/cpu_features/test/string_view_test.cc