Repositories list

• MSAvc

  Public
  C++

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• msawebsite

  Public
  website sources

  HTML

  •55 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• FMAlign2

  Public
  FMAlign2: A novel fast multiple nucleotide sequence alignment method for ultra-long datasets

  C++

  •

  Apache License 2.0

  •22 forks•88 stars•00 issues•00 pull requests•Updated Apr 3, 2026Apr 3, 2026

• benchmark_datasets_4_msa

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• HAlign-4

  Public
  HAlign 4: A New Strategy for Rapidly Aligning Millions of Sequences

  C++

  •

  MIT License

  •44 forks•88 stars•00 issues•00 pull requests•Updated Mar 11, 2026Mar 11, 2026

• spscore

  Public
  A fast, memory-efficient tool to calculate Sum-of-Pairs (SP) scores for Multiple Sequence Alignments (MSA).

  C++

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 3, 2026Feb 3, 2026

• Cax

  Public
  Python

  •

  MIT License

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jan 26, 2026Jan 26, 2026

• deMEM

  Public
  deMEM: a novel divide-and-conquer framework based on de Bruijn graph for scalable multiple sequence alignment

  C++

  •

  MIT License

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jan 13, 2026Jan 13, 2026

• linearPOA

  Public
  Memory-efficient Partial Order Alignment with linearPOA

  C++

  •11 fork•11 star•00 issues•00 pull requests•Updated Dec 24, 2025Dec 24, 2025

• HAlign-G

  Public
  A rapid and low-memory multiple-genome aligner for closely related genomes

  C++

  •

  MIT License

  •11 fork•2323 stars•00 issues•00 pull requests•Updated Sep 3, 2025Sep 3, 2025

• ReAlign-P

  Public
  🧬ReAlign-P: A vertical iterative realignment method for protein multiple sequence alignment

  C++

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 27, 2025Jun 27, 2025

• racon-with-simple-window

  Public
  C++

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 11, 2025Jun 11, 2025

• staccato

  Public
  C++11 Work-Stealing Task Scheduler

  C++

  •

  MIT License

  •33 forks•11 star•00 issues•00 pull requests•Updated Jun 11, 2025Jun 11, 2025

• TSTA

  Public
  pairwise and multiple sequence alignment accelerated by simd and threads

  C

  •

  MIT License

  •22 forks•11 star•00 issues•00 pull requests•Updated Apr 23, 2025Apr 23, 2025

• Chimera

  Public
  Chimera: A Versatile Metagenomic Classification Tool

  C

  •

  MIT License

  •22 forks•88 stars•00 issues•00 pull requests•Updated Apr 19, 2025Apr 19, 2025

• pbsim2

  Public
  PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores

  C++

  •

  GNU General Public License v2.0

  •1818 forks•00 stars•00 issues•00 pull requests•Updated Apr 1, 2025Apr 1, 2025

• MSATOOLS

  Public
  C++

  •33 forks•55 stars•00 issues•00 pull requests•Updated Apr 1, 2025Apr 1, 2025

• FORAlign

  Public
  FORAlign: Accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on FOur Russians approach with linear space complexity

  C

  •22 forks•22 stars•00 issues•00 pull requests•Updated Apr 1, 2025Apr 1, 2025

• SplitMEM_BWT

  Public
  SplitMEM submodule for deMEM

  C++

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 11, 2025Mar 11, 2025

• sdsl-lite-all-in-one

  Public
  Parallel suffix array calculation, used in SplitMEM

  C++

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 11, 2025Mar 11, 2025

• subhalign3

  Public
  HAlign 3 for deMEM

  Batchfile

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 10, 2025Mar 10, 2025

• submafft

  Public
  MAFFT Submodule for deMEM

  Shell

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 10, 2025Mar 10, 2025

• CaPS-SA

  Public
  Cache-friendly, Parallel, and Samplesort-based Constructor for Suffix Arrays and LCP Arrays

  C++

  •

  MIT License

  •77 forks•00 stars•00 issues•00 pull requests•Updated Mar 4, 2025Mar 4, 2025

• RaMA

  Public
  Fast sequence alignment for centromere with RaMA

  C++

  •

  Apache License 2.0

  •11 fork•33 stars•00 issues•00 pull requests•Updated Jan 31, 2025Jan 31, 2025

• FORAlign_testcase

  Public
  Test Data For FORAlign

  11 fork•00 stars•00 issues•00 pull requests•Updated Dec 30, 2024Dec 30, 2024

• ReAlign-N

  Public
  🧬ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments

  multiple-sequence-alignmentrealignment

  multiple-sequence-alignmentrealignment

  C++

  •

  GNU General Public License v3.0

  •00 forks•33 stars•00 issues•00 pull requests•Updated Dec 25, 2024Dec 25, 2024

• ReAlign-Star

  Public
  🌟ReAlign-Star: an optimized realignment method for multiple sequence alignment, targeting star algorithm tools

  C++

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 28, 2024Oct 28, 2024

• klib

  Public
  klib的代码以及部分教程

  C

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 10, 2024Jul 10, 2024

• SSW

  Public
  Complete Striped Smith Waterman Library with Windows & Linux

  C

  •120120 forks•00 stars•00 issues•00 pull requests•Updated Jun 17, 2024Jun 17, 2024

• TPMA

  Public
  ⚙️TPMA: a two pointers meta-alignment tool to ensemble different nucleic acid multiple sequence alignment results

  refinementmultiple-sequence-alignmentmeta-alignment

  refinementmultiple-sequence-alignmentmeta-alignment

  C++

  •

  MIT License

  •00 forks•88 stars•00 issues•00 pull requests•Updated Apr 9, 2024Apr 9, 2024