├── .github └── marv6.png ├── .gitmodules ├── CMakeLists.txt ├── LICENCE.md ├── README.md ├── azure-pipelines.yml ├── data ├── CMakeLists.txt ├── conterminatordna.sh └── conterminatorprotein.sh ├── example ├── dna.fas ├── dna.mapping ├── prots.fas └── prots.mapping ├── lib └── mmseqs │ ├── .cirrus.yml │ ├── .dockerignore │ ├── .gitattributes │ ├── .github │ ├── ISSUE_TEMPLATE.md │ ├── mmseqs2_logo.png │ └── workflows │ │ └── docker.yml │ ├── .gitignore │ ├── .gitmodules │ ├── CMakeLists.txt │ ├── Dockerfile │ ├── LICENSE.md │ ├── README.md │ ├── azure-pipelines.yml │ ├── cmake │ ├── AppendTargetProperty.cmake │ ├── CheckSSEFeatures.cmake │ ├── FindASan.cmake │ ├── FindAtomic.cmake │ ├── FindMSan.cmake │ ├── FindTSan.cmake │ ├── FindUBSan.cmake │ ├── GetGitRevisionDescription.cmake │ ├── GetGitRevisionDescription.cmake.in │ ├── MMseqsResourceCompiler.cmake │ ├── MMseqsSetupDerivedTarget.cmake │ ├── MMseqsSetupTest.cmake │ ├── checkshell.sh │ └── xxdi.pl │ ├── data │ ├── CMakeLists.txt │ ├── PAM10.out │ ├── PAM100.out │ ├── PAM110.out │ ├── PAM120.out │ ├── PAM130.out │ ├── PAM140.out │ ├── PAM150.out │ ├── PAM160.out │ ├── PAM170.out │ ├── PAM180.out │ ├── PAM190.out │ ├── PAM20.out │ ├── PAM30.out │ ├── PAM40.out │ ├── PAM50.out │ ├── PAM60.out │ ├── PAM70.out │ ├── PAM80.out │ ├── PAM90.out │ ├── VTML10.out │ ├── VTML120.out │ ├── VTML160.out │ ├── VTML20.out │ ├── VTML40.out │ ├── VTML80.out │ ├── blosum100.out │ ├── blosum30.out │ ├── blosum35.out │ ├── blosum40.out │ ├── blosum45.out │ ├── blosum50.out │ ├── blosum55.out │ ├── blosum60.out │ ├── blosum62.out │ ├── blosum65.out │ ├── blosum70.out │ ├── blosum75.out │ ├── blosum80.out │ ├── blosum85.out │ ├── blosum90.out │ ├── blosum95.out │ ├── nucleotide.out │ ├── resources │ │ ├── CMakeLists.txt │ │ ├── CovSeqidQscPercMinDiag.lib │ │ ├── CovSeqidQscPercMinDiagTargetCov.lib │ │ ├── ExpOpt3_8_polished.cs32.lib │ │ ├── K4000.crf │ │ ├── Library255_may17.lib │ │ ├── cs219.lib │ │ ├── krona_prelude.html │ │ ├── libPolished_8.lib │ │ ├── libPure_blosum62_255.lib │ │ ├── libPure_blosum62_32.lib │ │ └── result_viz_prelude.html.zst │ └── workflow │ │ ├── CMakeLists.txt │ │ ├── blastn.sh │ │ ├── blastp.sh │ │ ├── blastpgp.sh │ │ ├── cascaded_clustering.sh │ │ ├── clustering.sh │ │ ├── createindex.sh │ │ ├── createtaxdb.sh │ │ ├── databases.sh │ │ ├── easycluster.sh │ │ ├── easyrbh.sh │ │ ├── easysearch.sh │ │ ├── easytaxonomy.sh │ │ ├── enrich.sh │ │ ├── iterativepp.sh │ │ ├── linclust.sh │ │ ├── linsearch.sh │ │ ├── map.sh │ │ ├── multihitdb.sh │ │ ├── multihitsearch.sh │ │ ├── nucleotide_clustering.sh │ │ ├── rbh.sh │ │ ├── searchslicedtargetprofile.sh │ │ ├── searchtargetprofile.sh │ │ ├── taxonomy.sh │ │ ├── taxpercontig.sh │ │ ├── translated_search.sh │ │ ├── tsv2exprofiledb.sh │ │ └── update_clustering.sh │ ├── examples │ ├── DB.fasta │ └── QUERY.fasta │ ├── lib │ ├── alp │ │ ├── CMakeLists.txt │ │ ├── LICENSE │ │ ├── njn_approx.hpp │ │ ├── njn_doubletype.hpp │ │ ├── njn_dynprogprob.cpp │ │ ├── njn_dynprogprob.hpp │ │ ├── njn_dynprogproblim.cpp │ │ ├── njn_dynprogproblim.hpp │ │ ├── njn_dynprogprobproto.cpp │ │ ├── njn_dynprogprobproto.hpp │ │ ├── njn_function.hpp │ │ ├── njn_integer.hpp │ │ ├── njn_ioutil.cpp │ │ ├── njn_ioutil.hpp │ │ ├── njn_localmaxstat.cpp │ │ ├── njn_localmaxstat.hpp │ │ ├── njn_localmaxstatmatrix.cpp │ │ ├── njn_localmaxstatmatrix.hpp │ │ ├── njn_localmaxstatutil.cpp │ │ ├── njn_localmaxstatutil.hpp │ │ ├── njn_matrix.hpp │ │ ├── njn_memutil.hpp │ │ ├── njn_random.cpp │ │ ├── njn_random.hpp │ │ ├── njn_root.hpp │ │ ├── njn_uniform.hpp │ │ ├── njn_vector.hpp │ │ ├── readme.txt │ │ ├── sls_alignment_evaluer.cpp │ │ ├── sls_alignment_evaluer.hpp │ │ ├── sls_alp.cpp │ │ ├── sls_alp.hpp │ │ ├── sls_alp_data.cpp │ │ ├── sls_alp_data.hpp │ │ ├── sls_alp_regression.cpp │ │ ├── sls_alp_regression.hpp │ │ ├── sls_alp_sim.cpp │ │ ├── sls_alp_sim.hpp │ │ ├── sls_basic.cpp │ │ ├── sls_basic.hpp │ │ ├── sls_normal_distr_array.hpp │ │ ├── sls_pvalues.cpp │ │ └── sls_pvalues.hpp │ ├── base64 │ │ ├── LICENSE │ │ ├── README.md │ │ └── base64.h │ ├── cacode │ │ ├── CMakeLists.txt │ │ ├── LICENSE.LAST │ │ ├── LICENSE.NCBI │ │ ├── README │ │ ├── lambda_calculator.cpp │ │ ├── lambda_calculator.h │ │ ├── lubksb.cpp │ │ ├── ludcmp.cpp │ │ ├── nrutil.cpp │ │ └── nrutil.h │ ├── gzstream │ │ ├── LICENSE │ │ ├── README │ │ └── gzstream.h │ ├── ips4o │ │ ├── LICENSE │ │ ├── README.md │ │ ├── ips4o.hpp │ │ └── ips4o │ │ │ ├── base_case.hpp │ │ │ ├── block_permutation.hpp │ │ │ ├── bucket_pointers.hpp │ │ │ ├── buffers.hpp │ │ │ ├── classifier.hpp │ │ │ ├── cleanup_margins.hpp │ │ │ ├── config.hpp │ │ │ ├── empty_block_movement.hpp │ │ │ ├── ips4o.hpp │ │ │ ├── ips4o_fwd.hpp │ │ │ ├── local_classification.hpp │ │ │ ├── memory.hpp │ │ │ ├── parallel.hpp │ │ │ ├── partitioning.hpp │ │ │ ├── sampling.hpp │ │ │ ├── sequential.hpp │ │ │ ├── synchronization.hpp │ │ │ ├── thread_pool.hpp │ │ │ └── utils.hpp │ ├── ksw2 │ │ ├── CMakeLists.txt │ │ ├── LICENSE.txt │ │ ├── README.md │ │ ├── kseq.h │ │ ├── ksw2.h │ │ └── ksw2_extz2_sse.cpp │ ├── microtar │ │ ├── CMakeLists.txt │ │ ├── LICENSE │ │ ├── README.md │ │ ├── microtar.c │ │ └── microtar.h │ ├── nedmalloc │ │ ├── CMakeLists.txt │ │ ├── License.txt │ │ ├── Readme.txt │ │ ├── malloc.c.h │ │ ├── nedmalloc.c │ │ └── nedmalloc.h │ ├── omptl │ │ ├── Example.cpp │ │ ├── License.txt │ │ ├── algorithm │ │ ├── numeric │ │ ├── omptl │ │ ├── omptl_algorithm │ │ ├── omptl_algorithm_par.h │ │ ├── omptl_algorithm_ser.h │ │ ├── omptl_numeric │ │ ├── omptl_numeric_extensions.h │ │ ├── omptl_numeric_extensions_par.h │ │ ├── omptl_numeric_extensions_ser.h │ │ ├── omptl_numeric_par.h │ │ ├── omptl_numeric_ser.h │ │ └── omptl_tools.h │ ├── simd │ │ └── simd.h │ ├── simde │ │ └── simde │ │ │ ├── COPYING │ │ │ ├── README.md │ │ │ ├── arm │ │ │ ├── neon.h │ │ │ └── neon │ │ │ │ ├── aba.h │ │ │ │ ├── abd.h │ │ │ │ ├── abdl.h │ │ │ │ ├── abs.h │ │ │ │ ├── add.h │ │ │ │ ├── addl.h │ │ │ │ ├── addl_high.h │ │ │ │ ├── addlv.h │ │ │ │ ├── addv.h │ │ │ │ ├── addw.h │ │ │ │ ├── addw_high.h │ │ │ │ ├── and.h │ │ │ │ ├── bcax.h │ │ │ │ ├── bic.h │ │ │ │ ├── bsl.h │ │ │ │ ├── cage.h │ │ │ │ ├── cagt.h │ │ │ │ ├── ceq.h │ │ │ │ ├── ceqz.h │ │ │ │ ├── cge.h │ │ │ │ ├── cgez.h │ │ │ │ ├── cgt.h │ │ │ │ ├── cgtz.h │ │ │ │ ├── cle.h │ │ │ │ ├── clez.h │ │ │ │ ├── cls.h │ │ │ │ ├── clt.h │ │ │ │ ├── cltz.h │ │ │ │ ├── clz.h │ │ │ │ ├── cnt.h │ │ │ │ ├── combine.h │ │ │ │ ├── create.h │ │ │ │ ├── cvt.h │ │ │ │ ├── dot.h │ │ │ │ ├── dot_lane.h │ │ │ │ ├── dup_lane.h │ │ │ │ ├── dup_n.h │ │ │ │ ├── eor.h │ │ │ │ ├── ext.h │ │ │ │ ├── get_high.h │ │ │ │ ├── get_lane.h │ │ │ │ ├── get_low.h │ │ │ │ ├── hadd.h │ │ │ │ ├── hsub.h │ │ │ │ ├── ld1.h │ │ │ │ ├── ld3.h │ │ │ │ ├── ld4.h │ │ │ │ ├── max.h │ │ │ │ ├── maxnm.h │ │ │ │ ├── maxv.h │ │ │ │ ├── min.h │ │ │ │ ├── minnm.h │ │ │ │ ├── minv.h │ │ │ │ ├── mla.h │ │ │ │ ├── mla_n.h │ │ │ │ ├── mlal.h │ │ │ │ ├── mlal_high.h │ │ │ │ ├── mlal_n.h │ │ │ │ ├── mls.h │ │ │ │ ├── mlsl.h │ │ │ │ ├── mlsl_high.h │ │ │ │ ├── mlsl_n.h │ │ │ │ ├── movl.h │ │ │ │ ├── movl_high.h │ │ │ │ ├── movn.h │ │ │ │ ├── movn_high.h │ │ │ │ ├── mul.h │ │ │ │ ├── mul_lane.h │ │ │ │ ├── mul_n.h │ │ │ │ ├── mull.h │ │ │ │ ├── mull_high.h │ │ │ │ ├── mull_n.h │ │ │ │ ├── mvn.h │ │ │ │ ├── neg.h │ │ │ │ ├── orn.h │ │ │ │ ├── orr.h │ │ │ │ ├── padal.h │ │ │ │ ├── padd.h │ │ │ │ ├── paddl.h │ │ │ │ ├── pmax.h │ │ │ │ ├── pmin.h │ │ │ │ ├── qabs.h │ │ │ │ ├── qadd.h │ │ │ │ ├── qdmulh.h │ │ │ │ ├── qdmull.h │ │ │ │ ├── qmovn.h │ │ │ │ ├── qmovn_high.h │ │ │ │ ├── qmovun.h │ │ │ │ ├── qneg.h │ │ │ │ ├── qrdmulh.h │ │ │ │ ├── qrdmulh_n.h │ │ │ │ ├── qshl.h │ │ │ │ ├── qsub.h │ │ │ │ ├── qtbl.h │ │ │ │ ├── qtbx.h │ │ │ │ ├── rbit.h │ │ │ │ ├── reinterpret.h │ │ │ │ ├── rev16.h │ │ │ │ ├── rev32.h │ │ │ │ ├── rev64.h │ │ │ │ ├── rhadd.h │ │ │ │ ├── rnd.h │ │ │ │ ├── rndi.h │ │ │ │ ├── rndm.h │ │ │ │ ├── rndn.h │ │ │ │ ├── rndp.h │ │ │ │ ├── rshl.h │ │ │ │ ├── rshr_n.h │ │ │ │ ├── rsra_n.h │ │ │ │ ├── set_lane.h │ │ │ │ ├── shl.h │ │ │ │ ├── shl_n.h │ │ │ │ ├── shr_n.h │ │ │ │ ├── sqadd.h │ │ │ │ ├── sra_n.h │ │ │ │ ├── st1.h │ │ │ │ ├── st1_lane.h │ │ │ │ ├── st3.h │ │ │ │ ├── st4.h │ │ │ │ ├── sub.h │ │ │ │ ├── subl.h │ │ │ │ ├── subw.h │ │ │ │ ├── subw_high.h │ │ │ │ ├── tbl.h │ │ │ │ ├── tbx.h │ │ │ │ ├── trn.h │ │ │ │ ├── trn1.h │ │ │ │ ├── trn2.h │ │ │ │ ├── tst.h │ │ │ │ ├── types.h │ │ │ │ ├── uqadd.h │ │ │ │ ├── uzp.h │ │ │ │ ├── uzp1.h │ │ │ │ ├── uzp2.h │ │ │ │ ├── xar.h │ │ │ │ ├── zip.h │ │ │ │ ├── zip1.h │ │ │ │ └── zip2.h │ │ │ ├── check.h │ │ │ ├── debug-trap.h │ │ │ ├── hedley.h │ │ │ ├── simde-align.h │ │ │ ├── simde-arch.h │ │ │ ├── simde-common.h │ │ │ ├── simde-complex.h │ │ │ ├── simde-constify.h │ │ │ ├── simde-detect-clang.h │ │ │ ├── simde-diagnostic.h │ │ │ ├── simde-f16.h │ │ │ ├── simde-features.h │ │ │ ├── simde-math.h │ │ │ ├── wasm │ │ │ └── simd128.h │ │ │ └── x86 │ │ │ ├── avx.h │ │ │ ├── avx2.h │ │ │ ├── avx512.h │ │ │ ├── avx512 │ │ │ ├── 2intersect.h │ │ │ ├── abs.h │ │ │ ├── add.h │ │ │ ├── adds.h │ │ │ ├── and.h │ │ │ ├── andnot.h │ │ │ ├── avg.h │ │ │ ├── blend.h │ │ │ ├── broadcast.h │ │ │ ├── cast.h │ │ │ ├── cmp.h │ │ │ ├── cmpeq.h │ │ │ ├── cmpge.h │ │ │ ├── cmpgt.h │ │ │ ├── cmple.h │ │ │ ├── cmplt.h │ │ │ ├── copysign.h │ │ │ ├── cvt.h │ │ │ ├── cvts.h │ │ │ ├── div.h │ │ │ ├── extract.h │ │ │ ├── fmadd.h │ │ │ ├── fmsub.h │ │ │ ├── fnmadd.h │ │ │ ├── fnmsub.h │ │ │ ├── insert.h │ │ │ ├── kshift.h │ │ │ ├── load.h │ │ │ ├── loadu.h │ │ │ ├── lzcnt.h │ │ │ ├── madd.h │ │ │ ├── maddubs.h │ │ │ ├── max.h │ │ │ ├── min.h │ │ │ ├── mov.h │ │ │ ├── mov_mask.h │ │ │ ├── movm.h │ │ │ ├── mul.h │ │ │ ├── mulhi.h │ │ │ ├── mulhrs.h │ │ │ ├── mullo.h │ │ │ ├── negate.h │ │ │ ├── or.h │ │ │ ├── packs.h │ │ │ ├── packus.h │ │ │ ├── permutex2var.h │ │ │ ├── permutexvar.h │ │ │ ├── sad.h │ │ │ ├── set.h │ │ │ ├── set1.h │ │ │ ├── set4.h │ │ │ ├── setone.h │ │ │ ├── setr.h │ │ │ ├── setr4.h │ │ │ ├── setzero.h │ │ │ ├── shuffle.h │ │ │ ├── sll.h │ │ │ ├── slli.h │ │ │ ├── sllv.h │ │ │ ├── sqrt.h │ │ │ ├── sra.h │ │ │ ├── srai.h │ │ │ ├── srav.h │ │ │ ├── srl.h │ │ │ ├── srli.h │ │ │ ├── srlv.h │ │ │ ├── store.h │ │ │ ├── storeu.h │ │ │ ├── sub.h │ │ │ ├── subs.h │ │ │ ├── test.h │ │ │ ├── types.h │ │ │ ├── unpackhi.h │ │ │ ├── unpacklo.h │ │ │ ├── xor.h │ │ │ └── xorsign.h │ │ │ ├── clmul.h │ │ │ ├── f16c.h │ │ │ ├── fma.h │ │ │ ├── gfni.h │ │ │ ├── mmx.h │ │ │ ├── sse.h │ │ │ ├── sse2.h │ │ │ ├── sse3.h │ │ │ ├── sse4.1.h │ │ │ ├── sse4.2.h │ │ │ ├── ssse3.h │ │ │ ├── svml.h │ │ │ └── xop.h │ ├── tinyexpr │ │ ├── .travis.yml │ │ ├── CMakeLists.txt │ │ ├── CONTRIBUTING │ │ ├── LICENSE │ │ ├── Makefile │ │ ├── README.md │ │ ├── benchmark.c │ │ ├── doc │ │ │ ├── e1.dot │ │ │ ├── e1.png │ │ │ ├── e2.dot │ │ │ └── e2.png │ │ ├── example.c │ │ ├── example2.c │ │ ├── example3.c │ │ ├── minctest.h │ │ ├── test.c │ │ ├── tinyexpr.c │ │ └── tinyexpr.h │ ├── xxhash │ │ ├── LICENSE │ │ ├── xxhash.c │ │ └── xxhash.h │ └── zstd │ │ ├── .buckconfig │ │ ├── .buckversion │ │ ├── .circleci │ │ └── config.yml │ │ ├── .gitattributes │ │ ├── .gitignore │ │ ├── .travis.yml │ │ ├── CHANGELOG │ │ ├── CODE_OF_CONDUCT.md │ │ ├── CONTRIBUTING.md │ │ ├── COPYING │ │ ├── LICENSE │ │ ├── Makefile │ │ ├── README.md │ │ ├── TESTING.md │ │ ├── appveyor.yml │ │ ├── build │ │ ├── .gitignore │ │ ├── README.md │ │ ├── VS2008 │ │ │ ├── fullbench │ │ │ │ └── fullbench.vcproj │ │ │ ├── fuzzer │ │ │ │ └── fuzzer.vcproj │ │ │ ├── zstd.sln │ │ │ ├── zstd │ │ │ │ └── zstd.vcproj │ │ │ └── zstdlib │ │ │ │ └── zstdlib.vcproj │ │ ├── VS2010 │ │ │ ├── CompileAsCpp.props │ │ │ ├── datagen │ │ │ │ └── datagen.vcxproj │ │ │ ├── fullbench-dll │ │ │ │ └── fullbench-dll.vcxproj │ │ │ ├── fullbench │ │ │ │ └── fullbench.vcxproj │ │ │ ├── fuzzer │ │ │ │ └── fuzzer.vcxproj │ │ │ ├── libzstd-dll │ │ │ │ ├── libzstd-dll.rc │ │ │ │ └── libzstd-dll.vcxproj │ │ │ ├── libzstd │ │ │ │ └── libzstd.vcxproj │ │ │ ├── zstd.sln │ │ │ └── zstd │ │ │ │ ├── zstd.rc │ │ │ │ └── zstd.vcxproj │ │ ├── VS_scripts │ │ │ ├── README.md │ │ │ ├── build.VS2010.cmd │ │ │ ├── build.VS2012.cmd │ │ │ ├── build.VS2013.cmd │ │ │ ├── build.VS2015.cmd │ │ │ ├── build.VS2017.cmd │ │ │ ├── build.VS2017Community.cmd │ │ │ ├── build.VS2017Enterprise.cmd │ │ │ ├── build.VS2017Professional.cmd │ │ │ └── build.generic.cmd │ │ ├── cmake │ │ │ ├── .gitignore │ │ │ ├── CMakeLists.txt │ │ │ ├── CMakeModules │ │ │ │ ├── AddZstdCompilationFlags.cmake │ │ │ │ └── GetZstdLibraryVersion.cmake │ │ │ ├── contrib │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── gen_html │ │ │ │ │ └── CMakeLists.txt │ │ │ │ └── pzstd │ │ │ │ │ └── CMakeLists.txt │ │ │ ├── lib │ │ │ │ ├── .gitignore │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── cmake_uninstall.cmake.in │ │ │ │ └── pkgconfig.cmake │ │ │ ├── programs │ │ │ │ ├── .gitignore │ │ │ │ └── CMakeLists.txt │ │ │ └── tests │ │ │ │ ├── .gitignore │ │ │ │ └── CMakeLists.txt │ │ └── meson │ │ │ ├── GetZstdLibraryVersion.py │ │ │ ├── InstallSymlink.py │ │ │ ├── README.md │ │ │ ├── contrib │ │ │ ├── gen_html │ │ │ │ └── meson.build │ │ │ ├── meson.build │ │ │ └── pzstd │ │ │ │ └── meson.build │ │ │ ├── lib │ │ │ └── meson.build │ │ │ ├── meson.build │ │ │ ├── meson_options.txt │ │ │ ├── programs │ │ │ └── meson.build │ │ │ └── tests │ │ │ ├── meson.build │ │ │ └── valgrindTest.py │ │ ├── contrib │ │ ├── VS2005 │ │ │ ├── README.md │ │ │ ├── fullbench │ │ │ │ └── fullbench.vcproj │ │ │ ├── fuzzer │ │ │ │ └── fuzzer.vcproj │ │ │ ├── zstd.sln │ │ │ ├── zstd │ │ │ │ └── zstd.vcproj │ │ │ └── zstdlib │ │ │ │ └── zstdlib.vcproj │ │ ├── adaptive-compression │ │ │ ├── .gitignore │ │ │ ├── Makefile │ │ │ ├── README.md │ │ │ ├── adapt.c │ │ │ ├── datagencli.c │ │ │ ├── test-correctness.sh │ │ │ └── test-performance.sh │ │ ├── cleanTabs │ │ ├── docker │ │ │ ├── Dockerfile │ │ │ └── README.md │ │ ├── experimental_dict_builders │ │ │ ├── benchmarkDictBuilder │ │ │ │ ├── Makefile │ │ │ │ ├── README.md │ │ │ │ ├── benchmark.c │ │ │ │ ├── dictBuilder.h │ │ │ │ └── test.sh │ │ │ ├── fastCover │ │ │ │ ├── Makefile │ │ │ │ ├── README.md │ │ │ │ ├── fastCover.c │ │ │ │ ├── fastCover.h │ │ │ │ ├── main.c │ │ │ │ └── test.sh │ │ │ └── randomDictBuilder │ │ │ │ ├── Makefile │ │ │ │ ├── README.md │ │ │ │ ├── io.c │ │ │ │ ├── io.h │ │ │ │ ├── main.c │ │ │ │ ├── random.c │ │ │ │ ├── random.h │ │ │ │ └── test.sh │ │ ├── gen_html │ │ │ ├── .gitignore │ │ │ ├── Makefile │ │ │ ├── README.md │ │ │ ├── gen-zstd-manual.sh │ │ │ └── gen_html.cpp │ │ ├── largeNbDicts │ │ │ ├── .gitignore │ │ │ ├── Makefile │ │ │ ├── README.md │ │ │ └── largeNbDicts.c │ │ ├── linux-kernel │ │ │ ├── .gitignore │ │ │ ├── 0000-cover-letter.patch │ │ │ ├── 0001-lib-Add-xxhash-module.patch │ │ │ ├── 0002-lib-Add-zstd-modules.patch │ │ │ ├── 0003-btrfs-Add-zstd-support.patch │ │ │ ├── 0004-squashfs-Add-zstd-support.patch │ │ │ ├── 0005-crypto-Add-zstd-support.patch │ │ │ ├── 0006-squashfs-tools-Add-zstd-support.patch │ │ │ ├── COPYING │ │ │ ├── README.md │ │ │ ├── btrfs-benchmark.sh │ │ │ ├── btrfs-extract-benchmark.sh │ │ │ ├── fs │ │ │ │ ├── btrfs │ │ │ │ │ └── zstd.c │ │ │ │ └── squashfs │ │ │ │ │ └── zstd_wrapper.c │ │ │ ├── include │ │ │ │ └── linux │ │ │ │ │ ├── xxhash.h │ │ │ │ │ └── zstd.h │ │ │ ├── kernelize.sh │ │ │ ├── lib │ │ │ │ ├── Kconfig.diff │ │ │ │ ├── Makefile.diff │ │ │ │ ├── xxhash.c │ │ │ │ └── zstd │ │ │ │ │ ├── .clang-format │ │ │ │ │ ├── Makefile │ │ │ │ │ ├── bitstream.h │ │ │ │ │ ├── compress.c │ │ │ │ │ ├── decompress.c │ │ │ │ │ ├── entropy_common.c │ │ │ │ │ ├── error_private.h │ │ │ │ │ ├── fse.h │ │ │ │ │ ├── fse_compress.c │ │ │ │ │ ├── fse_decompress.c │ │ │ │ │ ├── huf.h │ │ │ │ │ ├── huf_compress.c │ │ │ │ │ ├── huf_decompress.c │ │ │ │ │ ├── mem.h │ │ │ │ │ ├── zstd_common.c │ │ │ │ │ ├── zstd_internal.h │ │ │ │ │ └── zstd_opt.h │ │ │ ├── squashfs-benchmark.sh │ │ │ ├── test │ │ │ │ ├── .gitignore │ │ │ │ ├── DecompressCrash.c │ │ │ │ ├── Makefile │ │ │ │ ├── RoundTripCrash.c │ │ │ │ ├── UserlandTest.cpp │ │ │ │ ├── XXHashUserlandTest.cpp │ │ │ │ └── include │ │ │ │ │ ├── asm │ │ │ │ │ └── unaligned.h │ │ │ │ │ └── linux │ │ │ │ │ ├── compiler.h │ │ │ │ │ ├── errno.h │ │ │ │ │ ├── kernel.h │ │ │ │ │ ├── math64.h │ │ │ │ │ ├── module.h │ │ │ │ │ ├── string.h │ │ │ │ │ └── types.h │ │ │ ├── xxhash_test.c │ │ │ ├── zstd_compress_test.c │ │ │ └── zstd_decompress_test.c │ │ ├── premake │ │ │ ├── premake4.lua │ │ │ └── zstd.lua │ │ ├── pzstd │ │ │ ├── .gitignore │ │ │ ├── BUCK │ │ │ ├── ErrorHolder.h │ │ │ ├── Logging.h │ │ │ ├── Makefile │ │ │ ├── Options.cpp │ │ │ ├── Options.h │ │ │ ├── Pzstd.cpp │ │ │ ├── Pzstd.h │ │ │ ├── README.md │ │ │ ├── SkippableFrame.cpp │ │ │ ├── SkippableFrame.h │ │ │ ├── images │ │ │ │ ├── Cspeed.png │ │ │ │ └── Dspeed.png │ │ │ ├── main.cpp │ │ │ ├── test │ │ │ │ ├── BUCK │ │ │ │ ├── OptionsTest.cpp │ │ │ │ ├── PzstdTest.cpp │ │ │ │ ├── RoundTrip.h │ │ │ │ └── RoundTripTest.cpp │ │ │ └── utils │ │ │ │ ├── BUCK │ │ │ │ ├── Buffer.h │ │ │ │ ├── FileSystem.h │ │ │ │ ├── Likely.h │ │ │ │ ├── Range.h │ │ │ │ ├── ResourcePool.h │ │ │ │ ├── ScopeGuard.h │ │ │ │ ├── ThreadPool.h │ │ │ │ ├── WorkQueue.h │ │ │ │ └── test │ │ │ │ ├── BUCK │ │ │ │ ├── BufferTest.cpp │ │ │ │ ├── RangeTest.cpp │ │ │ │ ├── ResourcePoolTest.cpp │ │ │ │ ├── ScopeGuardTest.cpp │ │ │ │ ├── ThreadPoolTest.cpp │ │ │ │ └── WorkQueueTest.cpp │ │ ├── seekable_format │ │ │ ├── examples │ │ │ │ ├── .gitignore │ │ │ │ ├── Makefile │ │ │ │ ├── parallel_compression.c │ │ │ │ ├── parallel_processing.c │ │ │ │ ├── seekable_compression.c │ │ │ │ └── seekable_decompression.c │ │ │ ├── zstd_seekable.h │ │ │ ├── zstd_seekable_compression_format.md │ │ │ ├── zstdseek_compress.c │ │ │ └── zstdseek_decompress.c │ │ └── snap │ │ │ └── snapcraft.yaml │ │ ├── doc │ │ ├── README.md │ │ ├── educational_decoder │ │ │ ├── Makefile │ │ │ ├── README.md │ │ │ ├── harness.c │ │ │ ├── zstd_decompress.c │ │ │ └── zstd_decompress.h │ │ ├── images │ │ │ ├── CSpeed2.png │ │ │ ├── DCspeed5.png │ │ │ ├── DSpeed3.png │ │ │ ├── cdict_v136.png │ │ │ ├── dict-cr.png │ │ │ ├── dict-cs.png │ │ │ ├── dict-ds.png │ │ │ ├── zstd_cdict_v1_3_5.png │ │ │ └── zstd_logo86.png │ │ ├── zstd_compression_format.md │ │ └── zstd_manual.html │ │ ├── examples │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── README.md │ │ ├── dictionary_compression.c │ │ ├── dictionary_decompression.c │ │ ├── multiple_streaming_compression.c │ │ ├── simple_compression.c │ │ ├── simple_decompression.c │ │ ├── streaming_compression.c │ │ ├── streaming_decompression.c │ │ └── streaming_memory_usage.c │ │ ├── lib │ │ ├── .gitignore │ │ ├── BUCK │ │ ├── Makefile │ │ ├── README.md │ │ ├── common │ │ │ ├── bitstream.h │ │ │ ├── compiler.h │ │ │ ├── cpu.h │ │ │ ├── debug.c │ │ │ ├── debug.h │ │ │ ├── entropy_common.c │ │ │ ├── error_private.c │ │ │ ├── error_private.h │ │ │ ├── fse.h │ │ │ ├── fse_decompress.c │ │ │ ├── huf.h │ │ │ ├── mem.h │ │ │ ├── pool.c │ │ │ ├── pool.h │ │ │ ├── threading.c │ │ │ ├── threading.h │ │ │ ├── xxhash.c │ │ │ ├── xxhash.h │ │ │ ├── zstd_common.c │ │ │ ├── zstd_errors.h │ │ │ └── zstd_internal.h │ │ ├── compress │ │ │ ├── fse_compress.c │ │ │ ├── hist.c │ │ │ ├── hist.h │ │ │ ├── huf_compress.c │ │ │ ├── zstd_compress.c │ │ │ ├── zstd_compress_internal.h │ │ │ ├── zstd_double_fast.c │ │ │ ├── zstd_double_fast.h │ │ │ ├── zstd_fast.c │ │ │ ├── zstd_fast.h │ │ │ ├── zstd_lazy.c │ │ │ ├── zstd_lazy.h │ │ │ ├── zstd_ldm.c │ │ │ ├── zstd_ldm.h │ │ │ ├── zstd_opt.c │ │ │ ├── zstd_opt.h │ │ │ ├── zstdmt_compress.c │ │ │ └── zstdmt_compress.h │ │ ├── decompress │ │ │ ├── huf_decompress.c │ │ │ ├── zstd_ddict.c │ │ │ ├── zstd_ddict.h │ │ │ ├── zstd_decompress.c │ │ │ ├── zstd_decompress_block.c │ │ │ ├── zstd_decompress_block.h │ │ │ └── zstd_decompress_internal.h │ │ ├── deprecated │ │ │ ├── zbuff.h │ │ │ ├── zbuff_common.c │ │ │ ├── zbuff_compress.c │ │ │ └── zbuff_decompress.c │ │ ├── dictBuilder │ │ │ ├── cover.c │ │ │ ├── cover.h │ │ │ ├── divsufsort.c │ │ │ ├── divsufsort.h │ │ │ ├── fastcover.c │ │ │ ├── zdict.c │ │ │ └── zdict.h │ │ ├── dll │ │ │ ├── example │ │ │ │ ├── Makefile │ │ │ │ ├── README.md │ │ │ │ ├── build_package.bat │ │ │ │ ├── fullbench-dll.sln │ │ │ │ └── fullbench-dll.vcxproj │ │ │ └── libzstd.def │ │ ├── legacy │ │ │ ├── zstd_legacy.h │ │ │ ├── zstd_v01.c │ │ │ ├── zstd_v01.h │ │ │ ├── zstd_v02.c │ │ │ ├── zstd_v02.h │ │ │ ├── zstd_v03.c │ │ │ ├── zstd_v03.h │ │ │ ├── zstd_v04.c │ │ │ ├── zstd_v04.h │ │ │ ├── zstd_v05.c │ │ │ ├── zstd_v05.h │ │ │ ├── zstd_v06.c │ │ │ ├── zstd_v06.h │ │ │ ├── zstd_v07.c │ │ │ └── zstd_v07.h │ │ ├── libzstd.pc.in │ │ └── zstd.h │ │ ├── programs │ │ ├── .gitignore │ │ ├── BUCK │ │ ├── Makefile │ │ ├── README.md │ │ ├── benchfn.c │ │ ├── benchfn.h │ │ ├── benchzstd.c │ │ ├── benchzstd.h │ │ ├── datagen.c │ │ ├── datagen.h │ │ ├── dibio.c │ │ ├── dibio.h │ │ ├── fileio.c │ │ ├── fileio.h │ │ ├── platform.h │ │ ├── util.c │ │ ├── util.h │ │ ├── windres │ │ │ ├── generate_res.bat │ │ │ ├── verrsrc.h │ │ │ ├── zstd.rc │ │ │ ├── zstd32.res │ │ │ └── zstd64.res │ │ ├── zstd.1 │ │ ├── zstd.1.md │ │ ├── zstdcli.c │ │ ├── zstdgrep │ │ ├── zstdgrep.1 │ │ ├── zstdgrep.1.md │ │ ├── zstdless │ │ ├── zstdless.1 │ │ └── zstdless.1.md │ │ ├── tests │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── README.md │ │ ├── checkTag.c │ │ ├── datagencli.c │ │ ├── decodecorpus.c │ │ ├── files │ │ │ └── huffman-compressed-larger │ │ ├── fullbench.c │ │ ├── fuzz │ │ │ ├── .gitignore │ │ │ ├── Makefile │ │ │ ├── README.md │ │ │ ├── block_decompress.c │ │ │ ├── block_round_trip.c │ │ │ ├── default.options │ │ │ ├── fuzz.h │ │ │ ├── fuzz.py │ │ │ ├── fuzz_helpers.h │ │ │ ├── regression_driver.c │ │ │ ├── simple_decompress.c │ │ │ ├── simple_round_trip.c │ │ │ ├── stream_decompress.c │ │ │ ├── stream_round_trip.c │ │ │ ├── zstd_helpers.c │ │ │ └── zstd_helpers.h │ │ ├── fuzzer.c │ │ ├── gzip │ │ │ ├── Makefile │ │ │ ├── gzip-env.sh │ │ │ ├── helin-segv.sh │ │ │ ├── help-version.sh │ │ │ ├── hufts-segv.gz │ │ │ ├── hufts.sh │ │ │ ├── init.cfg │ │ │ ├── init.sh │ │ │ ├── keep.sh │ │ │ ├── list.sh │ │ │ ├── memcpy-abuse.sh │ │ │ ├── mixed.sh │ │ │ ├── null-suffix-clobber.sh │ │ │ ├── stdin.sh │ │ │ ├── test-driver.sh │ │ │ ├── trailing-nul.sh │ │ │ ├── unpack-invalid.sh │ │ │ ├── z-suffix.sh │ │ │ ├── zdiff.sh │ │ │ ├── zgrep-context.sh │ │ │ ├── zgrep-f.sh │ │ │ ├── zgrep-signal.sh │ │ │ └── znew-k.sh │ │ ├── invalidDictionaries.c │ │ ├── legacy.c │ │ ├── libzstd_partial_builds.sh │ │ ├── longmatch.c │ │ ├── paramgrill.c │ │ ├── playTests.sh │ │ ├── poolTests.c │ │ ├── rateLimiter.py │ │ ├── regression │ │ │ ├── Makefile │ │ │ ├── config.c │ │ │ ├── config.h │ │ │ ├── data.c │ │ │ ├── data.h │ │ │ ├── levels.h │ │ │ ├── method.c │ │ │ ├── method.h │ │ │ ├── result.c │ │ │ ├── result.h │ │ │ ├── results.csv │ │ │ └── test.c │ │ ├── roundTripCrash.c │ │ ├── seqgen.c │ │ ├── seqgen.h │ │ ├── symbols.c │ │ ├── test-zstd-speed.py │ │ ├── test-zstd-versions.py │ │ ├── zbufftest.c │ │ └── zstreamtest.c │ │ └── zlibWrapper │ │ ├── .gitignore │ │ ├── BUCK │ │ ├── Makefile │ │ ├── README.md │ │ ├── examples │ │ ├── example.c │ │ ├── example_original.c │ │ ├── fitblk.c │ │ ├── fitblk_original.c │ │ ├── minigzip.c │ │ └── zwrapbench.c │ │ ├── gzclose.c │ │ ├── gzcompatibility.h │ │ ├── gzguts.h │ │ ├── gzlib.c │ │ ├── gzread.c │ │ ├── gzwrite.c │ │ ├── zstd_zlibwrapper.c │ │ └── zstd_zlibwrapper.h │ ├── src │ ├── CMakeLists.txt │ ├── CommandDeclarations.h │ ├── MMseqsBase.cpp │ ├── alignment │ │ ├── Alignment.cpp │ │ ├── Alignment.h │ │ ├── BandedNucleotideAligner.cpp │ │ ├── BandedNucleotideAligner.h │ │ ├── CMakeLists.txt │ │ ├── CompressedA3M.cpp │ │ ├── CompressedA3M.h │ │ ├── DistanceCalculator.h │ │ ├── EvalueComputation.h │ │ ├── Main.cpp │ │ ├── Matcher.cpp │ │ ├── Matcher.h │ │ ├── MsaFilter.cpp │ │ ├── MsaFilter.h │ │ ├── MultipleAlignment.cpp │ │ ├── MultipleAlignment.h │ │ ├── PSSMCalculator.cpp │ │ ├── PSSMCalculator.h │ │ ├── PSSMMasker.h │ │ ├── StripedSmithWaterman.cpp │ │ ├── StripedSmithWaterman.h │ │ └── rescorediagonal.cpp │ ├── clustering │ │ ├── AlignmentSymmetry.cpp │ │ ├── AlignmentSymmetry.h │ │ ├── CMakeLists.txt │ │ ├── Clustering.cpp │ │ ├── Clustering.h │ │ ├── ClusteringAlgorithms.cpp │ │ ├── ClusteringAlgorithms.h │ │ └── Main.cpp │ ├── commons │ │ ├── A3MReader.cpp │ │ ├── A3MReader.h │ │ ├── AminoAcidLookupTables.h │ │ ├── Application.cpp │ │ ├── BacktraceTranslator.h │ │ ├── BaseMatrix.cpp │ │ ├── BaseMatrix.h │ │ ├── ByteParser.h │ │ ├── CMakeLists.txt │ │ ├── CSProfile.cpp │ │ ├── CSProfile.h │ │ ├── Command.cpp │ │ ├── Command.h │ │ ├── CommandCaller.cpp │ │ ├── CommandCaller.h │ │ ├── Concat.h │ │ ├── DBConcat.cpp │ │ ├── DBConcat.h │ │ ├── DBReader.cpp │ │ ├── DBReader.h │ │ ├── DBWriter.cpp │ │ ├── DBWriter.h │ │ ├── Debug.cpp │ │ ├── Debug.h │ │ ├── Domain.h │ │ ├── DownloadDatabase.h │ │ ├── ExpressionParser.cpp │ │ ├── ExpressionParser.h │ │ ├── FastSort.h │ │ ├── FileUtil.cpp │ │ ├── FileUtil.h │ │ ├── HeaderSummarizer.cpp │ │ ├── HeaderSummarizer.h │ │ ├── IndexReader.h │ │ ├── IntervalArray.h │ │ ├── KSeqBufferReader.h │ │ ├── KSeqWrapper.cpp │ │ ├── KSeqWrapper.h │ │ ├── LibraryReader.cpp │ │ ├── LibraryReader.h │ │ ├── MMseqsMPI.cpp │ │ ├── MMseqsMPI.h │ │ ├── MathUtil.h │ │ ├── MemoryMapped.cpp │ │ ├── MemoryMapped.h │ │ ├── MemoryTracker.cpp │ │ ├── MemoryTracker.h │ │ ├── MultiParam.cpp │ │ ├── MultiParam.h │ │ ├── NucleotideMatrix.cpp │ │ ├── NucleotideMatrix.h │ │ ├── Orf.cpp │ │ ├── Orf.h │ │ ├── Parameters.cpp │ │ ├── Parameters.h │ │ ├── PatternCompiler.h │ │ ├── ProfileStates.cpp │ │ ├── ProfileStates.h │ │ ├── ScoreMatrix.h │ │ ├── Sequence.cpp │ │ ├── Sequence.h │ │ ├── StringBlock.h │ │ ├── SubstitutionMatrix.cpp │ │ ├── SubstitutionMatrix.h │ │ ├── SubstitutionMatrixProfileStates.h │ │ ├── Timer.h │ │ ├── TranslateNucl.h │ │ ├── UniprotKB.cpp │ │ ├── UniprotKB.h │ │ ├── Util.cpp │ │ ├── Util.h │ │ ├── itoa.h │ │ ├── tantan.cpp │ │ └── tantan.h │ ├── linclust │ │ ├── CMakeLists.txt │ │ ├── KmerIndex.h │ │ ├── LinsearchIndexReader.cpp │ │ ├── LinsearchIndexReader.h │ │ ├── MarkovKmerScore.h │ │ ├── kmerindexdb.cpp │ │ ├── kmermatcher.cpp │ │ ├── kmermatcher.h │ │ ├── kmersearch.cpp │ │ └── kmersearch.h │ ├── mmseqs.cpp │ ├── multihit │ │ ├── Aggregation.cpp │ │ ├── Aggregation.h │ │ ├── CMakeLists.txt │ │ ├── MultiHitDb.cpp │ │ ├── MultiHitSearch.cpp │ │ ├── besthitperset.cpp │ │ ├── combinepvalperset.cpp │ │ └── resultsbyset.cpp │ ├── prefiltering │ │ ├── CMakeLists.txt │ │ ├── CacheFriendlyOperations.cpp │ │ ├── CacheFriendlyOperations.h │ │ ├── ExtendedSubstitutionMatrix.cpp │ │ ├── ExtendedSubstitutionMatrix.h │ │ ├── IndexBuilder.cpp │ │ ├── IndexBuilder.h │ │ ├── IndexTable.h │ │ ├── Indexer.cpp │ │ ├── Indexer.h │ │ ├── KmerGenerator.cpp │ │ ├── KmerGenerator.h │ │ ├── Main.cpp │ │ ├── Prefiltering.cpp │ │ ├── Prefiltering.h │ │ ├── PrefilteringIndexReader.cpp │ │ ├── PrefilteringIndexReader.h │ │ ├── QueryMatcher.cpp │ │ ├── QueryMatcher.h │ │ ├── QueryMatcherTaxonomyHook.h │ │ ├── ReducedMatrix.cpp │ │ ├── ReducedMatrix.h │ │ ├── SequenceLookup.cpp │ │ ├── SequenceLookup.h │ │ ├── UngappedAlignment.cpp │ │ ├── UngappedAlignment.h │ │ └── ungappedprefilter.cpp │ ├── taxonomy │ │ ├── CMakeLists.txt │ │ ├── MappingReader.h │ │ ├── NcbiTaxonomy.cpp │ │ ├── NcbiTaxonomy.h │ │ ├── TaxonomyExpression.h │ │ ├── addtaxonomy.cpp │ │ ├── aggregatetax.cpp │ │ ├── createbintaxmapping.cpp │ │ ├── createbintaxonomy.cpp │ │ ├── createtaxdb.cpp │ │ ├── filtertaxdb.cpp │ │ ├── filtertaxseqdb.cpp │ │ ├── lca.cpp │ │ └── taxonomyreport.cpp │ ├── test │ │ ├── CMakeLists.txt │ │ ├── TestAlignment.cpp │ │ ├── TestAlignmentPerformance.cpp │ │ ├── TestAlignmentTraceback.cpp │ │ ├── TestAlp.cpp │ │ ├── TestBacktraceTranslator.cpp │ │ ├── TestBestAlphabet.cpp │ │ ├── TestCompositionBias.cpp │ │ ├── TestCounting.cpp │ │ ├── TestDBReader.cpp │ │ ├── TestDBReaderIndexSerialization.cpp │ │ ├── TestDBReaderZstd.cpp │ │ ├── TestDiagonalScoring.cpp │ │ ├── TestDiagonalScoringPerformance.cpp │ │ ├── TestExtendedSubstitutionMatrix.cpp │ │ ├── TestIndexTable.cpp │ │ ├── TestKmerGenerator.cpp │ │ ├── TestKmerGeneratorPerf.cpp │ │ ├── TestKmerGeneratorProfile.cpp │ │ ├── TestKmerNucl.cpp │ │ ├── TestKmerScore.cpp │ │ ├── TestKsw2.cpp │ │ ├── TestKwayMerge.cpp │ │ ├── TestMerge.cpp │ │ ├── TestMultipleAlignment.cpp │ │ ├── TestOrf.cpp │ │ ├── TestPSSM.cpp │ │ ├── TestPSSMPrune.cpp │ │ ├── TestProfileAlignment.cpp │ │ ├── TestReduceMatrix.cpp │ │ ├── TestScoreMatrixSerialization.cpp │ │ ├── TestSequenceIndex.cpp │ │ ├── TestTanTan.cpp │ │ ├── TestTaxExpr.cpp │ │ ├── TestTaxonomy.cpp │ │ ├── TestTinyExpr.cpp │ │ ├── TestTranslate.cpp │ │ ├── TestUtil.cpp │ │ ├── dataGap │ │ ├── dataGap.index │ │ ├── dataLinear │ │ └── dataLinear.index │ ├── util │ │ ├── CMakeLists.txt │ │ ├── alignall.cpp │ │ ├── alignbykmer.cpp │ │ ├── appenddbtoindex.cpp │ │ ├── apply.cpp │ │ ├── clusthash.cpp │ │ ├── compress.cpp │ │ ├── convert2fasta.cpp │ │ ├── convertalignments.cpp │ │ ├── convertca3m.cpp │ │ ├── convertkb.cpp │ │ ├── convertmsa.cpp │ │ ├── convertprofiledb.cpp │ │ ├── countkmer.cpp │ │ ├── cpmvrmlndb.cpp │ │ ├── createdb.cpp │ │ ├── createseqfiledb.cpp │ │ ├── createsubdb.cpp │ │ ├── createtsv.cpp │ │ ├── db2tar.cpp │ │ ├── dbtype.cpp │ │ ├── diffseqdbs.cpp │ │ ├── diskspaceavail.cpp │ │ ├── expandaln.cpp │ │ ├── extractalignedregion.cpp │ │ ├── extractdomains.cpp │ │ ├── extractframes.cpp │ │ ├── extractorfs.cpp │ │ ├── filterdb.cpp │ │ ├── gff2db.cpp │ │ ├── indexdb.cpp │ │ ├── maskbygff.cpp │ │ ├── masksequence.cpp │ │ ├── mergeclusters.cpp │ │ ├── mergedbs.cpp │ │ ├── mergeresultsbyset.cpp │ │ ├── msa2profile.cpp │ │ ├── msa2result.cpp │ │ ├── nrtotaxmapping.cpp │ │ ├── offsetalignment.cpp │ │ ├── orftocontig.cpp │ │ ├── pairaln.cpp │ │ ├── prefixid.cpp │ │ ├── profile2pssm.cpp │ │ ├── profile2seq.cpp │ │ ├── proteinaln2nucl.cpp │ │ ├── renamedbkeys.cpp │ │ ├── result2dnamsa.cpp │ │ ├── result2flat.cpp │ │ ├── result2msa.cpp │ │ ├── result2profile.cpp │ │ ├── result2rbh.cpp │ │ ├── result2repseq.cpp │ │ ├── result2stats.cpp │ │ ├── result2stats.h │ │ ├── reverseseq.cpp │ │ ├── sequence2profile.cpp │ │ ├── sortresult.cpp │ │ ├── splitdb.cpp │ │ ├── splitsequence.cpp │ │ ├── subtractdbs.cpp │ │ ├── summarizealis.cpp │ │ ├── summarizeheaders.cpp │ │ ├── summarizeresult.cpp │ │ ├── summarizetabs.cpp │ │ ├── swapresults.cpp │ │ ├── tar2db.cpp │ │ ├── touchdb.cpp │ │ ├── transitivealign.cpp │ │ ├── translateaa.cpp │ │ ├── translatenucs.cpp │ │ ├── tsv2db.cpp │ │ ├── tsv2exprofiledb.cpp │ │ ├── unpackdb.cpp │ │ ├── versionstring.cpp │ │ └── view.cpp │ ├── version │ │ ├── CMakeLists.txt │ │ └── Version.cpp │ └── workflow │ │ ├── CMakeLists.txt │ │ ├── Cluster.cpp │ │ ├── ClusterUpdate.cpp │ │ ├── CreateIndex.cpp │ │ ├── Databases.cpp │ │ ├── EasyCluster.cpp │ │ ├── EasyLinclust.cpp │ │ ├── EasyRbh.cpp │ │ ├── EasySearch.cpp │ │ ├── EasyTaxonomy.cpp │ │ ├── Enrich.cpp │ │ ├── Linclust.cpp │ │ ├── Linsearch.cpp │ │ ├── Map.cpp │ │ ├── Rbh.cpp │ │ ├── Search.cpp │ │ └── Taxonomy.cpp │ └── util │ ├── .gitattributes │ ├── CMakeLists.txt │ ├── bash-completion.sh │ ├── build_osx.sh │ ├── build_windows.sh │ ├── format_substitution_matrix.R │ ├── make-release.sh │ ├── mmseqs_wrapper.bat │ ├── mmseqs_wrapper.sh │ ├── update_simde.sh │ └── update_zstd.sh └── src ├── CMakeLists.txt ├── commons ├── CMakeLists.txt ├── IntervalArray.h ├── KingdomExpression.h ├── LocalCommandDeclarations.h ├── LocalParameters.cpp └── LocalParameters.h ├── conterminator.cpp ├── conterminatorutils ├── CMakeLists.txt ├── TaxonUtils.h ├── createallreport.cpp ├── createstats.cpp ├── crosstaxonfilter.cpp ├── crosstaxonfilterorf.cpp ├── extractalignments.cpp └── predictcontamination.cpp ├── version ├── CMakeLists.txt └── Version.cpp └── workflow ├── CMakeLists.txt ├── Conterminatordna.cpp └── Conterminatorprotein.cpp 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