├── .github └── workflows │ └── ci.yaml ├── .gitignore ├── Cargo.toml ├── LICENSE ├── README.md ├── benches ├── prefix_scan.rs └── rand_scan.rs ├── block_aligner_modes.png ├── c ├── Cargo.toml ├── Makefile ├── README.md ├── block_aligner.h ├── cbindgen.toml └── example.c ├── data ├── README.md ├── uc30_0.95_pairwise_aln.sh └── uc30_pairwise_aln.sh ├── examples ├── accuracy.rs ├── block_img.rs ├── compare.rs ├── debug.rs ├── nanopore_accuracy.rs ├── nanopore_bench.rs ├── nanopore_bench_global.rs ├── profile.rs ├── pssm_accuracy.rs ├── pssm_bench.rs ├── uc_accuracy.rs ├── uc_bench.rs ├── verify_trace.rs └── x_drop_accuracy.rs ├── ideas.md ├── matrices ├── BLOSUM45 ├── BLOSUM50 ├── BLOSUM62 ├── BLOSUM80 ├── BLOSUM90 ├── NW1 ├── PAM100 ├── PAM120 ├── PAM160 ├── PAM200 └── PAM250 ├── rust-toolchain ├── scripts ├── accuracy_avx2.sh ├── accuracy_wasm.sh ├── bench_avx2.sh ├── bench_wasm.sh ├── build_ir_asm.sh ├── build_wat.sh ├── compare_avx2.sh ├── create_matrix_aa.py ├── create_matrix_nuc.py ├── debug_avx2.sh ├── doc_avx2.sh ├── doc_wasm.sh ├── nanopore_accuracy_avx2.sh ├── nanopore_bench_avx2.sh ├── nanopore_bench_global_avx2.sh ├── pssm_accuracy_avx2.sh ├── pssm_bench_avx2.sh ├── scop_seq_profile_pairs.py ├── simulate_k.py ├── test_avx2.sh ├── test_wasm.sh ├── uc_accuracy_avx2.sh ├── uc_bench_avx2.sh └── x_drop_accuracy_avx2.sh ├── src ├── avx2.rs ├── cigar.rs ├── ffi.rs ├── lib.rs ├── neon.rs ├── old │ ├── scan_band.rs │ ├── scan_block_old.rs │ ├── scan_minecraft.rs │ └── scan_thin.rs ├── scan_block.rs ├── scores.rs ├── simd128.rs └── sse2.rs └── vis ├── block_aligner_accuracy_vis.ipynb ├── block_aligner_bench_vis.ipynb ├── block_img1.png ├── block_img2.png ├── compare_adaptive_banding.pdf ├── compare_diagonal.pdf ├── dna_global_bench.pdf ├── nanopore_10kbp_largest_gap.pdf ├── nanopore_10kbp_scores.pdf ├── nanopore_50kbp_largest_gap.pdf ├── nanopore_50kbp_scores.pdf ├── nanopore_bench.pdf ├── prefix_scan_bench.pdf ├── pssm_accuracy.pdf ├── pssm_scores.pdf ├── 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