├── .github └── workflows │ ├── autotools-cross.yml │ ├── autotools.yml │ ├── cmake.yml │ └── meson.yml ├── .gitignore ├── CHANGELOG.md ├── CMakeLists.txt ├── DISCLAIMER ├── LICENSE.md ├── Makefile.am ├── README.md ├── apps ├── README.md ├── meson.build ├── parasail_aligner.cpp └── parasail_stats.c ├── appveyor.yml ├── cmake ├── FindAVX2.cmake ├── FindAltiVec.cmake ├── FindNEON.cmake ├── FindSSE2.cmake ├── FindSSE41.cmake ├── Findxgetbv.cmake ├── altivec_dummy.c ├── avx2_dummy.c ├── config.h.in ├── neon_dummy.c ├── parasail.def ├── parasail.ico ├── sse2_dummy.c ├── sse41_dummy.c ├── ssw_dummy.c └── toolchain-arm-linux-gnueabi.cmake ├── configure.ac ├── contrib ├── PW_sequence_alignment_2015.pdf ├── cpuid.c ├── cpuid_gen4.c ├── getMemorySize.c ├── kseq.h ├── meson.build ├── sais-lite-lcp │ ├── COPYING │ ├── Makefile │ ├── README │ ├── sais.c │ ├── sais.h │ ├── sais.hxx │ ├── suftest.c │ └── test.c ├── simde │ ├── .appveyor.yml │ ├── .gitignore │ ├── .gitmodules │ ├── .travis.yml │ ├── COPYING │ ├── README.md │ ├── simde │ │ ├── arm │ │ │ ├── neon.h │ │ │ └── neon │ │ │ │ ├── float32x2.h │ │ │ │ ├── float32x4.h │ │ │ │ ├── float64x1.h │ │ │ │ ├── float64x2.h │ │ │ │ ├── int16x4.h │ │ │ │ ├── int16x8.h │ │ │ │ ├── int32x2.h │ │ │ │ ├── int32x4.h │ │ │ │ ├── int64x1.h │ │ │ │ ├── int64x2.h │ │ │ │ ├── int8x16.h │ │ │ │ ├── int8x8.h │ │ │ │ ├── uint16x4.h │ │ │ │ ├── uint16x8.h │ │ │ │ ├── uint32x2.h │ │ │ │ ├── uint32x4.h │ │ │ │ ├── uint64x1.h │ │ │ │ ├── uint64x2.h │ │ │ │ ├── uint8x16.h │ │ │ │ └── uint8x8.h │ │ ├── hedley.h │ │ ├── simd-js │ │ │ ├── bool32x4.h │ │ │ ├── float32x4.h │ │ │ ├── int32x4.h │ │ │ └── simd-js.h │ │ ├── simde-arch.h │ │ ├── simde-common.h │ │ └── x86 │ │ │ ├── avx.h │ │ │ ├── avx2.h │ │ │ ├── mmx.h │ │ │ ├── sse.h │ │ │ ├── sse2.h │ │ │ ├── sse3.h │ │ │ ├── sse4.1.h │ │ │ ├── sse4.2.h │ │ │ └── ssse3.h │ └── test │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ ├── arm │ │ ├── arm-internal.h │ │ └── neon │ │ │ ├── skel.c │ │ │ ├── vadd.c │ │ │ └── vdup_n.c │ │ ├── cmake │ │ ├── AddCompilerFlags.cmake │ │ ├── ExtraWarningFlags.cmake │ │ ├── toolchain-aarch64-linux-gnu.cmake │ │ └── toolchain-arm-linux-gnueabihf.cmake │ │ ├── simd-js │ │ ├── float32x4.c │ │ ├── int32x4-compare.c │ │ ├── int32x4.c │ │ ├── simd-js.h │ │ └── skel.c │ │ ├── test-common.c │ │ ├── test.c │ │ ├── test.h │ │ └── x86 │ │ ├── avx │ │ └── avx.c │ │ ├── avx2 │ │ └── avx2.c │ │ ├── compare.h │ │ ├── mmx │ │ ├── compare.c │ │ └── mmx.c │ │ ├── skel.c │ │ ├── sse │ │ ├── compare.c │ │ └── sse.c │ │ ├── sse2 │ │ ├── compare.c │ │ └── sse2.c │ │ ├── sse3 │ │ └── sse3.c │ │ ├── sse4.1 │ │ └── sse4.1.c │ │ ├── sse4.2 │ │ └── sse4.2.c │ │ ├── ssse3 │ │ └── ssse3.c │ │ └── x86-internal.h ├── ssw │ ├── main.c │ ├── ssw.c │ └── ssw.h └── wingetopt │ ├── .gitignore │ ├── CMakeLists.txt │ ├── README.md │ └── src │ ├── getopt.c │ └── getopt.h ├── data ├── O29181.fasta ├── O60341.fasta ├── P00762.fasta ├── P01008.fasta ├── P01111.fasta ├── P02232.fasta ├── P03435.fasta ├── P03630.fasta ├── P03989.fasta ├── P04775.fasta ├── P05013.fasta ├── P07327.fasta ├── P07756.fasta ├── P08519.fasta ├── P0C6B8.fasta ├── P10635.fasta ├── P14942.fasta ├── P19096.fasta ├── P20930.fasta ├── P21177.fasta ├── P25705.fasta ├── P27895.fasta ├── P28167.fasta ├── P33450.fasta ├── P42357.fasta ├── P53765.fasta ├── P56980.fasta ├── P58229.fasta ├── Q7TMA5.fasta ├── Q8ZGB4.fasta ├── Q9UKN1.fasta ├── cd02249_matrix.txt ├── cd02249_matrix_noquery.txt ├── cd02249_matrix_safe.txt ├── test_64.fasta ├── test_64r.fasta ├── test_P0_10.fasta ├── test_P0_2.fasta ├── test_P0_3.fasta ├── test_P0_4.fasta ├── test_P0_5.fasta ├── test_case.fasta ├── test_case2.fasta ├── test_p29.fasta ├── test_p59.fasta └── test_small_2.fasta ├── images ├── perf_haswell.png └── perf_mac.png ├── m4 ├── ax_check_compile_flag.m4 ├── ax_compiler_vendor.m4 ├── ax_compiler_version.m4 ├── ax_create_pkgconfig_info.m4 ├── ax_gcc_builtin.m4 ├── ax_openmp.m4 └── ax_recursive_eval.m4 ├── meson.build ├── meson_options.txt ├── parasail.h ├── parasail ├── cpuid.h ├── function_lookup.h ├── internal_altivec.h ├── internal_avx.h ├── internal_neon.h ├── internal_sse.h ├── io.h ├── matrices │ ├── blosum100.h │ ├── blosum30.h │ ├── blosum35.h │ ├── blosum40.h │ ├── blosum45.h │ ├── blosum50.h │ ├── blosum55.h │ ├── blosum60.h │ ├── blosum62.h │ ├── blosum65.h │ ├── blosum70.h │ ├── blosum75.h │ ├── blosum80.h │ ├── blosum85.h │ ├── blosum90.h │ ├── blosum_map.h │ ├── blosumn.h │ ├── dnafull.h │ ├── nuc44.h │ ├── pam10.h │ ├── pam100.h │ ├── pam110.h │ ├── pam120.h │ ├── pam130.h │ ├── pam140.h │ ├── pam150.h │ ├── pam160.h │ ├── pam170.h │ ├── pam180.h │ ├── pam190.h │ ├── pam20.h │ ├── pam200.h │ ├── pam210.h │ ├── pam220.h │ ├── pam230.h │ ├── pam240.h │ ├── pam250.h │ ├── pam260.h │ ├── pam270.h │ ├── pam280.h │ ├── pam290.h │ ├── pam30.h │ ├── pam300.h │ ├── pam310.h │ ├── pam320.h │ ├── pam330.h │ ├── pam340.h │ ├── pam350.h │ ├── pam360.h │ ├── pam370.h │ ├── pam380.h │ ├── pam390.h │ ├── pam40.h │ ├── pam400.h │ ├── pam410.h │ ├── pam420.h │ ├── pam430.h │ ├── pam440.h │ ├── pam450.h │ ├── pam460.h │ ├── pam470.h │ ├── pam480.h │ ├── pam490.h │ ├── pam50.h │ ├── pam500.h │ ├── pam60.h │ ├── pam70.h │ ├── pam80.h │ ├── pam90.h │ └── pam_map.h ├── matrix_lookup.h ├── memory.h ├── meson.build └── stats.h ├── performance.md ├── src ├── cigar.c ├── cigar_template.c ├── cpuid.c ├── dispatch_profile.c ├── dummy.c ├── function_lookup.c ├── io.c ├── isastubs.c ├── matrix_lookup.c ├── memory.c ├── memory.c.orig ├── memory_altivec.c ├── memory_avx2.c ├── memory_neon.c ├── memory_sse.c ├── meson.build ├── nw.c ├── nw_banded.c ├── nw_diag_altivec_128_16.c ├── nw_diag_altivec_128_32.c ├── nw_diag_altivec_128_64.c ├── nw_diag_altivec_128_8.c ├── nw_diag_avx2_256_16.c ├── nw_diag_avx2_256_32.c ├── nw_diag_avx2_256_64.c ├── nw_diag_avx2_256_8.c ├── nw_diag_neon_128_16.c ├── nw_diag_neon_128_32.c ├── nw_diag_neon_128_64.c ├── nw_diag_neon_128_8.c ├── nw_diag_sse2_128_16.c ├── nw_diag_sse2_128_32.c ├── nw_diag_sse2_128_64.c ├── nw_diag_sse2_128_8.c ├── nw_diag_sse41_128_16.c ├── nw_diag_sse41_128_32.c ├── nw_diag_sse41_128_64.c ├── nw_diag_sse41_128_8.c ├── nw_dispatch.c ├── nw_scan.c ├── nw_scan_altivec_128_16.c ├── nw_scan_altivec_128_32.c ├── nw_scan_altivec_128_64.c ├── nw_scan_altivec_128_8.c ├── nw_scan_avx2_256_16.c ├── nw_scan_avx2_256_32.c ├── nw_scan_avx2_256_64.c ├── nw_scan_avx2_256_8.c ├── nw_scan_neon_128_16.c ├── nw_scan_neon_128_32.c ├── nw_scan_neon_128_64.c ├── nw_scan_neon_128_8.c ├── nw_scan_sse2_128_16.c ├── nw_scan_sse2_128_32.c ├── nw_scan_sse2_128_64.c ├── nw_scan_sse2_128_8.c ├── nw_scan_sse41_128_16.c ├── nw_scan_sse41_128_32.c ├── nw_scan_sse41_128_64.c ├── nw_scan_sse41_128_8.c ├── nw_stats.c ├── nw_stats_diag_altivec_128_16.c ├── nw_stats_diag_altivec_128_32.c ├── nw_stats_diag_altivec_128_64.c ├── nw_stats_diag_altivec_128_8.c ├── nw_stats_diag_avx2_256_16.c ├── nw_stats_diag_avx2_256_32.c ├── nw_stats_diag_avx2_256_64.c ├── nw_stats_diag_avx2_256_8.c ├── nw_stats_diag_neon_128_16.c ├── nw_stats_diag_neon_128_32.c ├── nw_stats_diag_neon_128_64.c ├── nw_stats_diag_neon_128_8.c ├── nw_stats_diag_sse2_128_16.c ├── nw_stats_diag_sse2_128_32.c ├── nw_stats_diag_sse2_128_64.c ├── nw_stats_diag_sse2_128_8.c ├── nw_stats_diag_sse41_128_16.c ├── nw_stats_diag_sse41_128_32.c ├── nw_stats_diag_sse41_128_64.c ├── nw_stats_diag_sse41_128_8.c ├── nw_stats_scan.c ├── nw_stats_scan_altivec_128_16.c ├── nw_stats_scan_altivec_128_32.c ├── nw_stats_scan_altivec_128_64.c ├── nw_stats_scan_altivec_128_8.c ├── nw_stats_scan_avx2_256_16.c ├── nw_stats_scan_avx2_256_32.c ├── nw_stats_scan_avx2_256_64.c ├── nw_stats_scan_avx2_256_8.c ├── nw_stats_scan_neon_128_16.c ├── nw_stats_scan_neon_128_32.c ├── nw_stats_scan_neon_128_64.c ├── nw_stats_scan_neon_128_8.c ├── nw_stats_scan_sse2_128_16.c ├── nw_stats_scan_sse2_128_32.c ├── nw_stats_scan_sse2_128_64.c ├── nw_stats_scan_sse2_128_8.c ├── nw_stats_scan_sse41_128_16.c ├── nw_stats_scan_sse41_128_32.c ├── nw_stats_scan_sse41_128_64.c ├── nw_stats_scan_sse41_128_8.c ├── nw_stats_striped_altivec_128_16.c ├── nw_stats_striped_altivec_128_32.c ├── nw_stats_striped_altivec_128_64.c ├── nw_stats_striped_altivec_128_8.c ├── nw_stats_striped_avx2_256_16.c ├── nw_stats_striped_avx2_256_32.c ├── nw_stats_striped_avx2_256_64.c ├── nw_stats_striped_avx2_256_8.c ├── nw_stats_striped_neon_128_16.c ├── nw_stats_striped_neon_128_32.c ├── nw_stats_striped_neon_128_64.c ├── nw_stats_striped_neon_128_8.c ├── nw_stats_striped_sse2_128_16.c ├── nw_stats_striped_sse2_128_32.c ├── nw_stats_striped_sse2_128_64.c ├── nw_stats_striped_sse2_128_8.c ├── nw_stats_striped_sse41_128_16.c ├── nw_stats_striped_sse41_128_32.c ├── nw_stats_striped_sse41_128_64.c ├── nw_stats_striped_sse41_128_8.c ├── nw_striped_altivec_128_16.c ├── nw_striped_altivec_128_32.c ├── nw_striped_altivec_128_64.c ├── nw_striped_altivec_128_8.c ├── nw_striped_avx2_256_16.c ├── nw_striped_avx2_256_32.c ├── nw_striped_avx2_256_64.c ├── nw_striped_avx2_256_8.c ├── nw_striped_neon_128_16.c ├── nw_striped_neon_128_32.c ├── nw_striped_neon_128_64.c ├── nw_striped_neon_128_8.c ├── nw_striped_sse2_128_16.c ├── nw_striped_sse2_128_32.c ├── nw_striped_sse2_128_64.c ├── nw_striped_sse2_128_8.c ├── nw_striped_sse41_128_16.c ├── nw_striped_sse41_128_32.c ├── nw_striped_sse41_128_64.c ├── nw_striped_sse41_128_8.c ├── nw_trace.c ├── nw_trace_diag_altivec_128_16.c ├── nw_trace_diag_altivec_128_32.c ├── nw_trace_diag_altivec_128_64.c ├── nw_trace_diag_altivec_128_8.c ├── nw_trace_diag_avx2_256_16.c ├── nw_trace_diag_avx2_256_32.c ├── nw_trace_diag_avx2_256_64.c ├── nw_trace_diag_avx2_256_8.c ├── nw_trace_diag_neon_128_16.c ├── nw_trace_diag_neon_128_32.c ├── nw_trace_diag_neon_128_64.c ├── nw_trace_diag_neon_128_8.c ├── nw_trace_diag_sse2_128_16.c ├── nw_trace_diag_sse2_128_32.c ├── nw_trace_diag_sse2_128_64.c ├── nw_trace_diag_sse2_128_8.c ├── nw_trace_diag_sse41_128_16.c ├── nw_trace_diag_sse41_128_32.c ├── nw_trace_diag_sse41_128_64.c ├── nw_trace_diag_sse41_128_8.c ├── nw_trace_scan.c ├── nw_trace_scan_altivec_128_16.c ├── nw_trace_scan_altivec_128_32.c ├── nw_trace_scan_altivec_128_64.c ├── nw_trace_scan_altivec_128_8.c ├── nw_trace_scan_avx2_256_16.c ├── nw_trace_scan_avx2_256_32.c ├── nw_trace_scan_avx2_256_64.c ├── nw_trace_scan_avx2_256_8.c ├── nw_trace_scan_neon_128_16.c ├── nw_trace_scan_neon_128_32.c ├── nw_trace_scan_neon_128_64.c ├── nw_trace_scan_neon_128_8.c ├── nw_trace_scan_sse2_128_16.c ├── nw_trace_scan_sse2_128_32.c ├── nw_trace_scan_sse2_128_64.c ├── nw_trace_scan_sse2_128_8.c ├── nw_trace_scan_sse41_128_16.c ├── nw_trace_scan_sse41_128_32.c ├── nw_trace_scan_sse41_128_64.c ├── nw_trace_scan_sse41_128_8.c ├── nw_trace_striped_altivec_128_16.c ├── nw_trace_striped_altivec_128_32.c ├── nw_trace_striped_altivec_128_64.c ├── nw_trace_striped_altivec_128_8.c ├── nw_trace_striped_avx2_256_16.c ├── nw_trace_striped_avx2_256_32.c ├── nw_trace_striped_avx2_256_64.c ├── nw_trace_striped_avx2_256_8.c ├── nw_trace_striped_neon_128_16.c ├── nw_trace_striped_neon_128_32.c ├── nw_trace_striped_neon_128_64.c ├── nw_trace_striped_neon_128_8.c ├── nw_trace_striped_sse2_128_16.c ├── nw_trace_striped_sse2_128_32.c ├── nw_trace_striped_sse2_128_64.c ├── nw_trace_striped_sse2_128_8.c ├── nw_trace_striped_sse41_128_16.c ├── nw_trace_striped_sse41_128_32.c ├── nw_trace_striped_sse41_128_64.c ├── nw_trace_striped_sse41_128_8.c ├── parser.c ├── pssw.c ├── satcheck.c ├── sg.c ├── sg_db_dispatch.c ├── sg_de_dispatch.c ├── sg_diag_altivec_128_16.c ├── sg_diag_altivec_128_32.c ├── sg_diag_altivec_128_64.c ├── sg_diag_altivec_128_8.c ├── sg_diag_avx2_256_16.c ├── sg_diag_avx2_256_32.c ├── sg_diag_avx2_256_64.c ├── sg_diag_avx2_256_8.c ├── sg_diag_neon_128_16.c ├── sg_diag_neon_128_32.c ├── sg_diag_neon_128_64.c ├── sg_diag_neon_128_8.c ├── sg_diag_sse2_128_16.c ├── sg_diag_sse2_128_32.c ├── sg_diag_sse2_128_64.c ├── sg_diag_sse2_128_8.c ├── sg_diag_sse41_128_16.c ├── sg_diag_sse41_128_32.c ├── sg_diag_sse41_128_64.c ├── sg_diag_sse41_128_8.c ├── sg_dispatch.c ├── sg_dx_dispatch.c ├── sg_helper.h ├── sg_qb_db_dispatch.c ├── sg_qb_de_dispatch.c ├── sg_qb_dispatch.c ├── sg_qe_db_dispatch.c ├── sg_qe_de_dispatch.c ├── sg_qe_dispatch.c ├── sg_qx_dispatch.c ├── sg_scan.c ├── sg_scan_altivec_128_16.c ├── sg_scan_altivec_128_32.c ├── sg_scan_altivec_128_64.c ├── sg_scan_altivec_128_8.c ├── sg_scan_avx2_256_16.c ├── sg_scan_avx2_256_32.c ├── sg_scan_avx2_256_64.c ├── sg_scan_avx2_256_8.c ├── sg_scan_neon_128_16.c ├── sg_scan_neon_128_32.c ├── sg_scan_neon_128_64.c ├── sg_scan_neon_128_8.c ├── sg_scan_sse2_128_16.c ├── sg_scan_sse2_128_32.c ├── sg_scan_sse2_128_64.c ├── sg_scan_sse2_128_8.c ├── sg_scan_sse41_128_16.c ├── sg_scan_sse41_128_32.c ├── sg_scan_sse41_128_64.c ├── sg_scan_sse41_128_8.c ├── sg_stats.c ├── sg_stats_diag_altivec_128_16.c ├── sg_stats_diag_altivec_128_32.c ├── sg_stats_diag_altivec_128_64.c ├── sg_stats_diag_altivec_128_8.c ├── sg_stats_diag_avx2_256_16.c ├── sg_stats_diag_avx2_256_32.c ├── sg_stats_diag_avx2_256_64.c ├── sg_stats_diag_avx2_256_8.c ├── sg_stats_diag_neon_128_16.c ├── sg_stats_diag_neon_128_32.c ├── sg_stats_diag_neon_128_64.c ├── sg_stats_diag_neon_128_8.c ├── sg_stats_diag_sse2_128_16.c ├── sg_stats_diag_sse2_128_32.c ├── sg_stats_diag_sse2_128_64.c ├── sg_stats_diag_sse2_128_8.c ├── sg_stats_diag_sse41_128_16.c ├── sg_stats_diag_sse41_128_32.c ├── sg_stats_diag_sse41_128_64.c ├── sg_stats_diag_sse41_128_8.c ├── sg_stats_scan.c ├── sg_stats_scan_altivec_128_16.c ├── sg_stats_scan_altivec_128_32.c ├── sg_stats_scan_altivec_128_64.c ├── sg_stats_scan_altivec_128_8.c ├── sg_stats_scan_avx2_256_16.c ├── sg_stats_scan_avx2_256_32.c ├── sg_stats_scan_avx2_256_64.c ├── sg_stats_scan_avx2_256_8.c ├── sg_stats_scan_neon_128_16.c ├── sg_stats_scan_neon_128_32.c ├── sg_stats_scan_neon_128_64.c ├── sg_stats_scan_neon_128_8.c ├── sg_stats_scan_sse2_128_16.c ├── sg_stats_scan_sse2_128_32.c ├── sg_stats_scan_sse2_128_64.c ├── sg_stats_scan_sse2_128_8.c ├── sg_stats_scan_sse41_128_16.c ├── sg_stats_scan_sse41_128_32.c ├── sg_stats_scan_sse41_128_64.c ├── sg_stats_scan_sse41_128_8.c ├── sg_stats_striped_altivec_128_16.c ├── sg_stats_striped_altivec_128_32.c ├── sg_stats_striped_altivec_128_64.c ├── sg_stats_striped_altivec_128_8.c ├── sg_stats_striped_avx2_256_16.c ├── sg_stats_striped_avx2_256_32.c ├── sg_stats_striped_avx2_256_64.c ├── sg_stats_striped_avx2_256_8.c ├── sg_stats_striped_neon_128_16.c ├── sg_stats_striped_neon_128_32.c ├── sg_stats_striped_neon_128_64.c ├── sg_stats_striped_neon_128_8.c ├── sg_stats_striped_sse2_128_16.c ├── sg_stats_striped_sse2_128_32.c ├── sg_stats_striped_sse2_128_64.c ├── sg_stats_striped_sse2_128_8.c ├── sg_stats_striped_sse41_128_16.c ├── sg_stats_striped_sse41_128_32.c ├── sg_stats_striped_sse41_128_64.c ├── sg_stats_striped_sse41_128_8.c ├── sg_striped_altivec_128_16.c ├── sg_striped_altivec_128_32.c ├── sg_striped_altivec_128_64.c ├── sg_striped_altivec_128_8.c ├── sg_striped_avx2_256_16.c ├── sg_striped_avx2_256_32.c ├── sg_striped_avx2_256_64.c ├── sg_striped_avx2_256_8.c ├── sg_striped_neon_128_16.c ├── sg_striped_neon_128_32.c ├── sg_striped_neon_128_64.c ├── sg_striped_neon_128_8.c ├── sg_striped_sse2_128_16.c ├── sg_striped_sse2_128_32.c ├── sg_striped_sse2_128_64.c ├── sg_striped_sse2_128_8.c ├── sg_striped_sse41_128_16.c ├── sg_striped_sse41_128_32.c ├── sg_striped_sse41_128_64.c ├── sg_striped_sse41_128_8.c ├── sg_trace.c ├── sg_trace_diag_altivec_128_16.c ├── sg_trace_diag_altivec_128_32.c ├── sg_trace_diag_altivec_128_64.c ├── sg_trace_diag_altivec_128_8.c ├── sg_trace_diag_avx2_256_16.c ├── sg_trace_diag_avx2_256_32.c ├── sg_trace_diag_avx2_256_64.c ├── sg_trace_diag_avx2_256_8.c ├── sg_trace_diag_neon_128_16.c ├── sg_trace_diag_neon_128_32.c ├── sg_trace_diag_neon_128_64.c ├── sg_trace_diag_neon_128_8.c ├── sg_trace_diag_sse2_128_16.c ├── sg_trace_diag_sse2_128_32.c ├── sg_trace_diag_sse2_128_64.c ├── sg_trace_diag_sse2_128_8.c ├── sg_trace_diag_sse41_128_16.c ├── sg_trace_diag_sse41_128_32.c ├── sg_trace_diag_sse41_128_64.c ├── sg_trace_diag_sse41_128_8.c ├── sg_trace_scan.c ├── sg_trace_scan_altivec_128_16.c ├── sg_trace_scan_altivec_128_32.c ├── sg_trace_scan_altivec_128_64.c ├── sg_trace_scan_altivec_128_8.c ├── sg_trace_scan_avx2_256_16.c ├── sg_trace_scan_avx2_256_32.c ├── sg_trace_scan_avx2_256_64.c ├── sg_trace_scan_avx2_256_8.c ├── sg_trace_scan_neon_128_16.c ├── sg_trace_scan_neon_128_32.c ├── sg_trace_scan_neon_128_64.c ├── sg_trace_scan_neon_128_8.c ├── sg_trace_scan_sse2_128_16.c ├── sg_trace_scan_sse2_128_32.c ├── sg_trace_scan_sse2_128_64.c ├── sg_trace_scan_sse2_128_8.c ├── sg_trace_scan_sse41_128_16.c ├── sg_trace_scan_sse41_128_32.c ├── sg_trace_scan_sse41_128_64.c ├── sg_trace_scan_sse41_128_8.c ├── sg_trace_striped_altivec_128_16.c ├── sg_trace_striped_altivec_128_32.c ├── sg_trace_striped_altivec_128_64.c ├── sg_trace_striped_altivec_128_8.c ├── sg_trace_striped_avx2_256_16.c ├── sg_trace_striped_avx2_256_32.c ├── sg_trace_striped_avx2_256_64.c ├── sg_trace_striped_avx2_256_8.c ├── sg_trace_striped_neon_128_16.c ├── sg_trace_striped_neon_128_32.c ├── sg_trace_striped_neon_128_64.c ├── sg_trace_striped_neon_128_8.c ├── sg_trace_striped_sse2_128_16.c ├── sg_trace_striped_sse2_128_32.c ├── sg_trace_striped_sse2_128_64.c ├── sg_trace_striped_sse2_128_8.c ├── sg_trace_striped_sse41_128_16.c ├── sg_trace_striped_sse41_128_32.c ├── sg_trace_striped_sse41_128_64.c ├── sg_trace_striped_sse41_128_8.c ├── striped_unwind.c ├── sw.c ├── sw_blocked_sse41_128_16.c ├── sw_blocked_sse41_128_32.c ├── sw_diag_altivec_128_16.c ├── sw_diag_altivec_128_32.c ├── sw_diag_altivec_128_64.c ├── sw_diag_altivec_128_8.c ├── sw_diag_avx2_256_16.c ├── sw_diag_avx2_256_32.c ├── sw_diag_avx2_256_64.c ├── sw_diag_avx2_256_8.c ├── sw_diag_neon_128_16.c ├── sw_diag_neon_128_32.c ├── sw_diag_neon_128_64.c ├── sw_diag_neon_128_8.c ├── sw_diag_sse2_128_16.c ├── sw_diag_sse2_128_32.c ├── sw_diag_sse2_128_64.c ├── sw_diag_sse2_128_8.c ├── sw_diag_sse41_128_16.c ├── sw_diag_sse41_128_32.c ├── sw_diag_sse41_128_64.c ├── sw_diag_sse41_128_8.c ├── sw_dispatch.c ├── sw_scan.c ├── sw_scan_altivec_128_16.c ├── sw_scan_altivec_128_32.c ├── sw_scan_altivec_128_64.c ├── sw_scan_altivec_128_8.c ├── sw_scan_avx2_256_16.c ├── sw_scan_avx2_256_32.c ├── sw_scan_avx2_256_64.c ├── sw_scan_avx2_256_8.c ├── sw_scan_neon_128_16.c ├── sw_scan_neon_128_32.c ├── sw_scan_neon_128_64.c ├── sw_scan_neon_128_8.c ├── sw_scan_sse2_128_16.c ├── sw_scan_sse2_128_32.c ├── sw_scan_sse2_128_64.c ├── sw_scan_sse2_128_8.c ├── sw_scan_sse41_128_16.c ├── sw_scan_sse41_128_32.c ├── sw_scan_sse41_128_64.c ├── sw_scan_sse41_128_8.c ├── sw_stats.c ├── sw_stats_diag_altivec_128_16.c ├── sw_stats_diag_altivec_128_32.c ├── sw_stats_diag_altivec_128_64.c ├── sw_stats_diag_altivec_128_8.c ├── sw_stats_diag_avx2_256_16.c ├── sw_stats_diag_avx2_256_32.c ├── sw_stats_diag_avx2_256_64.c ├── sw_stats_diag_avx2_256_8.c ├── sw_stats_diag_neon_128_16.c ├── sw_stats_diag_neon_128_32.c ├── sw_stats_diag_neon_128_64.c ├── sw_stats_diag_neon_128_8.c ├── sw_stats_diag_sse2_128_16.c ├── sw_stats_diag_sse2_128_32.c ├── sw_stats_diag_sse2_128_64.c ├── sw_stats_diag_sse2_128_8.c ├── sw_stats_diag_sse41_128_16.c ├── sw_stats_diag_sse41_128_32.c ├── sw_stats_diag_sse41_128_64.c ├── sw_stats_diag_sse41_128_8.c ├── sw_stats_scan.c ├── sw_stats_scan_altivec_128_16.c ├── sw_stats_scan_altivec_128_32.c ├── sw_stats_scan_altivec_128_64.c ├── sw_stats_scan_altivec_128_8.c ├── sw_stats_scan_avx2_256_16.c ├── sw_stats_scan_avx2_256_32.c ├── sw_stats_scan_avx2_256_64.c ├── sw_stats_scan_avx2_256_8.c ├── sw_stats_scan_neon_128_16.c ├── sw_stats_scan_neon_128_32.c ├── sw_stats_scan_neon_128_64.c ├── sw_stats_scan_neon_128_8.c ├── sw_stats_scan_sse2_128_16.c ├── sw_stats_scan_sse2_128_32.c ├── sw_stats_scan_sse2_128_64.c ├── sw_stats_scan_sse2_128_8.c ├── sw_stats_scan_sse41_128_16.c ├── sw_stats_scan_sse41_128_32.c ├── sw_stats_scan_sse41_128_64.c ├── sw_stats_scan_sse41_128_8.c ├── sw_stats_striped_altivec_128_16.c ├── sw_stats_striped_altivec_128_32.c ├── sw_stats_striped_altivec_128_64.c ├── sw_stats_striped_altivec_128_8.c ├── sw_stats_striped_avx2_256_16.c ├── sw_stats_striped_avx2_256_32.c ├── sw_stats_striped_avx2_256_64.c ├── sw_stats_striped_avx2_256_8.c ├── sw_stats_striped_neon_128_16.c ├── sw_stats_striped_neon_128_32.c ├── sw_stats_striped_neon_128_64.c ├── sw_stats_striped_neon_128_8.c ├── sw_stats_striped_sse2_128_16.c ├── sw_stats_striped_sse2_128_32.c ├── sw_stats_striped_sse2_128_64.c ├── sw_stats_striped_sse2_128_8.c ├── sw_stats_striped_sse41_128_16.c ├── sw_stats_striped_sse41_128_32.c ├── sw_stats_striped_sse41_128_64.c ├── sw_stats_striped_sse41_128_8.c ├── sw_striped_altivec_128_16.c ├── sw_striped_altivec_128_32.c ├── sw_striped_altivec_128_64.c ├── sw_striped_altivec_128_8.c ├── sw_striped_avx2_256_16.c ├── sw_striped_avx2_256_32.c ├── sw_striped_avx2_256_64.c ├── sw_striped_avx2_256_8.c ├── sw_striped_neon_128_16.c ├── sw_striped_neon_128_32.c ├── sw_striped_neon_128_64.c ├── sw_striped_neon_128_8.c ├── sw_striped_sse2_128_16.c ├── sw_striped_sse2_128_32.c ├── sw_striped_sse2_128_64.c ├── sw_striped_sse2_128_8.c ├── sw_striped_sse41_128_16.c ├── sw_striped_sse41_128_32.c ├── sw_striped_sse41_128_64.c ├── sw_striped_sse41_128_8.c ├── sw_trace.c ├── sw_trace_diag_altivec_128_16.c ├── sw_trace_diag_altivec_128_32.c ├── sw_trace_diag_altivec_128_64.c ├── sw_trace_diag_altivec_128_8.c ├── sw_trace_diag_avx2_256_16.c ├── sw_trace_diag_avx2_256_32.c ├── sw_trace_diag_avx2_256_64.c ├── sw_trace_diag_avx2_256_8.c ├── sw_trace_diag_neon_128_16.c ├── sw_trace_diag_neon_128_32.c ├── sw_trace_diag_neon_128_64.c ├── sw_trace_diag_neon_128_8.c ├── sw_trace_diag_sse2_128_16.c ├── sw_trace_diag_sse2_128_32.c ├── sw_trace_diag_sse2_128_64.c ├── sw_trace_diag_sse2_128_8.c ├── sw_trace_diag_sse41_128_16.c ├── sw_trace_diag_sse41_128_32.c ├── sw_trace_diag_sse41_128_64.c ├── sw_trace_diag_sse41_128_8.c ├── sw_trace_scan.c ├── sw_trace_scan_altivec_128_16.c ├── sw_trace_scan_altivec_128_32.c ├── sw_trace_scan_altivec_128_64.c ├── sw_trace_scan_altivec_128_8.c ├── sw_trace_scan_avx2_256_16.c ├── sw_trace_scan_avx2_256_32.c ├── sw_trace_scan_avx2_256_64.c ├── sw_trace_scan_avx2_256_8.c ├── sw_trace_scan_neon_128_16.c ├── sw_trace_scan_neon_128_32.c ├── sw_trace_scan_neon_128_64.c ├── sw_trace_scan_neon_128_8.c ├── sw_trace_scan_sse2_128_16.c ├── sw_trace_scan_sse2_128_32.c ├── sw_trace_scan_sse2_128_64.c ├── sw_trace_scan_sse2_128_8.c ├── sw_trace_scan_sse41_128_16.c ├── sw_trace_scan_sse41_128_32.c ├── sw_trace_scan_sse41_128_64.c ├── sw_trace_scan_sse41_128_8.c ├── sw_trace_striped_altivec_128_16.c ├── sw_trace_striped_altivec_128_32.c ├── sw_trace_striped_altivec_128_64.c ├── sw_trace_striped_altivec_128_8.c ├── sw_trace_striped_avx2_256_16.c ├── sw_trace_striped_avx2_256_32.c ├── sw_trace_striped_avx2_256_64.c ├── sw_trace_striped_avx2_256_8.c ├── sw_trace_striped_neon_128_16.c ├── sw_trace_striped_neon_128_32.c ├── sw_trace_striped_neon_128_64.c ├── sw_trace_striped_neon_128_8.c ├── sw_trace_striped_sse2_128_16.c ├── sw_trace_striped_sse2_128_32.c ├── sw_trace_striped_sse2_128_64.c ├── sw_trace_striped_sse2_128_8.c ├── sw_trace_striped_sse41_128_16.c ├── sw_trace_striped_sse41_128_32.c ├── sw_trace_striped_sse41_128_64.c ├── sw_trace_striped_sse41_128_8.c ├── time.c ├── traceback.c └── traceback_template.c ├── tests ├── func_verify.h ├── func_verify_rowcols.h ├── func_verify_tables.h ├── func_verify_traces.h ├── meson.build ├── ssw_vs_pssw.c ├── test_12.c ├── test_64.c ├── test_align.c ├── test_altivec.c ├── test_basic.c ├── test_gcups.c ├── test_io.c ├── test_isa.c ├── test_matrix.c ├── test_openmp.c ├── test_openmp_sais.cpp ├── test_p29.c ├── test_p59.c ├── test_p59.h ├── test_pssm.c ├── test_query.c ├── test_scatter.c ├── test_ssw.cpp ├── test_sw_dispatch.c ├── test_verify.c ├── test_verify.test ├── test_verify_cigars.c ├── test_verify_rowcols.c ├── test_verify_tables.c ├── test_verify_traces.c ├── timer.h ├── timer_real.h └── traceback.c ├── travis └── build-docker.sh ├── util ├── codegen.py ├── diff_all.sh ├── dispatch_profile.py ├── dispatcher.py ├── func_group_rowcols.py ├── func_group_tables.py ├── func_group_traces.py ├── func_groups.py ├── funcs.py ├── gap_tester.py ├── isa.py ├── isastubs.py ├── makedef.py ├── matrices │ ├── BLOSUM100 │ ├── BLOSUM30 │ ├── BLOSUM35 │ ├── BLOSUM40 │ ├── BLOSUM45 │ ├── BLOSUM50 │ ├── BLOSUM55 │ ├── BLOSUM60 │ ├── BLOSUM62 │ ├── BLOSUM65 │ ├── BLOSUM70 │ ├── BLOSUM75 │ ├── BLOSUM80 │ ├── BLOSUM85 │ ├── BLOSUM90 │ ├── BLOSUMN │ ├── DAYHOFF │ ├── EDNAFULL │ ├── GONNET │ ├── NUC.4.4 │ ├── PAM10 │ ├── PAM100 │ ├── PAM110 │ ├── PAM120 │ ├── PAM130 │ ├── PAM140 │ ├── PAM150 │ ├── PAM160 │ ├── PAM170 │ ├── PAM180 │ ├── PAM190 │ ├── PAM20 │ ├── PAM200 │ ├── PAM210 │ ├── PAM220 │ ├── PAM230 │ ├── PAM240 │ ├── PAM250 │ ├── PAM260 │ ├── PAM270 │ ├── PAM280 │ ├── PAM290 │ ├── PAM30 │ ├── PAM300 │ ├── PAM310 │ ├── PAM320 │ ├── PAM330 │ ├── PAM340 │ ├── PAM350 │ ├── PAM360 │ ├── PAM370 │ ├── PAM380 │ ├── PAM390 │ ├── PAM40 │ ├── PAM400 │ ├── PAM410 │ ├── PAM420 │ ├── PAM430 │ ├── PAM440 │ ├── PAM450 │ ├── PAM460 │ ├── PAM470 │ ├── PAM480 │ ├── PAM490 │ ├── PAM50 │ ├── PAM500 │ ├── PAM60 │ ├── PAM70 │ ├── PAM80 │ ├── PAM90 │ ├── README │ └── codegen.py ├── memory.py ├── names.py ├── satcheck.py ├── templates │ ├── nw_diag.c │ ├── nw_scan.c │ ├── nw_stats_diag.c │ ├── nw_stats_scan.c │ ├── nw_stats_striped.c │ ├── nw_striped.c │ ├── nw_trace_diag.c │ ├── nw_trace_scan.c │ ├── nw_trace_striped.c │ ├── sg_diag.c │ ├── sg_diag_8.c │ ├── sg_scan.c │ ├── sg_stats_diag.c │ ├── sg_stats_scan.c │ ├── sg_stats_striped.c │ ├── sg_striped.c │ ├── sg_trace_diag.c │ ├── sg_trace_diag_8.c │ ├── sg_trace_scan.c │ ├── sg_trace_striped.c │ ├── sw_diag.c │ ├── sw_diag_8.c │ ├── sw_scan.c │ ├── sw_stats_diag.c │ ├── sw_stats_diag_8.c │ ├── sw_stats_scan.c │ ├── sw_stats_striped.c │ ├── sw_stats_striped_bias.c │ ├── sw_striped.c │ ├── sw_striped_bias.c │ ├── sw_trace_diag.c │ ├── sw_trace_diag_8.c │ ├── sw_trace_scan.c │ └── sw_trace_striped.c └── tester.py └── version.sh /.github/workflows/autotools.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffdaily/parasail/HEAD/.github/workflows/autotools.yml -------------------------------------------------------------------------------- /.github/workflows/cmake.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffdaily/parasail/HEAD/.github/workflows/cmake.yml -------------------------------------------------------------------------------- /.github/workflows/meson.yml: -------------------------------------------------------------------------------- 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