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abpoa

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

cd-hit-modified

This CD-HIT is a part of other programs.

fmalign2

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

foralign

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

foralign_testcase

Test Data For FORAlign

gmgc-data

Global Microbial Gene Catalog sequence data which stored separately according to sequence length

halign-2

a multiple sequence alignment tool

halign-3

do multiple nucleotide sequence alignment fast and accurately

halign-3-dataset

Dataset used from HAlign 3

halign-g

A rapid and low-memory multiple-genome aligner for thousands of human genomes

halign-g-data

A rapid and low-memory multiple-genome aligner for thousands of human genomes

hiv-data

HIV sequence data which stored separately according to sequence length

jmsa

for DNA/RNA MSA

jtmsa

Sequence alignment learning materials with python

klib

klib的代码以及部分教程

kseq

kseq: a generic stream buffer & FASTA/FASTQ file parser by @lh3

mpoxvr_dataset

MPox Virus sequence dataset

msatools

msavc

msawebsite

website sources

needleman-wunsch

Needleman-Wunsch algorithm visualisation for stmsa.

parallel-suffixarray

parallel suffix Array implementation: parallel DC3 & ParallelRange

qscore

Compares a multiple alignment with a reference and reports accuracy scores.

quantest2

QuanTest2 using Q Score and TC Score

rama

Fast sequence alignment for centromere with RaMA

realign-n

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

sreformat

Sreformat is a component of SQUID, which can convert various file types

sswfindsim

Use ssw method find similarity

stmsa-cpp

do multiple nucleotide sequence alignment fast and accurately

tpma

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