- [Bowtie2] - [C++, v2.5.4, 2024.05] - [2012.03, Nat Methods] - [Fast gapped-read alignment with Bowtie 2.]
- [bwa] - [C, v0.7.18, 2024.04] - [2009.05, Bioinformatics] - [Fast and accurate short read alignment with Burrows-Wheeler transform.]
- [bbmap] - [Java, v39.10, 2024.09] - [2014.03, No. LBNL-7065E] - [BBMap: A Fast, Accurate, Splice-Aware Aligner]
- BWA-MEM - [C, v0.7.18, 2024.04] - [2013.5, arXiv] - [Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM.]
- BWA-MEM2 - [C++, v2.2.1, 2021.3] - [2019.5, IEEE Parallel and Distributed Processing Symposium (IPDPS)] - [Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.]
- [Minimap2] - [C, v2.28, 2024.03] - [2018.05, Bioinformatics] - [Minimap2: pairwise alignment for nucleotide sequences.]
- [blast+] - [C++, 2.16.0, 2024.06] - [2009, BMC Bioinformatics] - [BLAST+: architecture and applications.] - [download BLAST databases.]
- [DIAMOND] - [C++, v0.9.25及以下, 2019.07] - [2015.1, Nat Methods] - [Fast and sensitive protein alignment using DIAMOND]
- [DIAMOND] - [C++, v2.1.9, 2024.01] - [2021.04, Nat Methods] - [Sensitive protein alignments at tree-of-life scale using DIAMOND]
- [LexicMap] - [Go, v0.4.0, 2024.08] - [2024.08, bioRxiv] [LexicMap: efficient sequence alignment against millions of prokaryotic genomes.]
- [foldmason] - [C/C++, v1-763a428, 2024.08] - [2024.08, bioRxiv] - [Multiple Protein Structure Alignment at Scale with FoldMason.]
- [MUSCLE] - [C++, v5.2, 2024.08] - [2022.11, Nat Commun] - [Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny] - Benchmark
- [SSU-ALIGN] - [Perl, v0.1.1, 2016.02] - [2009, Ph.D thesis, Washington U] - [Structural RNA Homology Search and Alignment Using Covariance Models]
- MAFFT - [C, v7.526, 2024.04] - [2013.01, Mol Biol Evol] - [MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability]
- [Clustal 2] - [NA, v2.1, 2010.10] - [2007.11, Bioinformatics] - [Clustal W and Clustal X version 2.0]
- [T-Coffee] - [C/Perl, 13.46.1.b8b01e06, 2024.6] - [2000.09, J Mol Biol] - [T-Coffee: a novel method for fast and accurate multiple sequence alignment]
- MMseq - [C++, Not Dev Anymore, 2016.9] - [2016.5, Bioinformatics] - MMseqs software suite for fast and deep clustering and searching of large protein sequence sets
- MMseq2 - [C/C++, 15-6f452, 2023.10] - [2017.11, Nat Biotechnol] - MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
- [MMseq2] - [CUDA GPU-based] - [2024.11, bioRxiv] - GPU-accelerated homology search with MMseqs2. - NVIDIA log
- USEARCH - [C++/C, v12.0-beta1, 2024.6] - [2010.10, Bioinformatics] - Search and clustering orders of magnitude faster than BLAST
- USEARCH - [C++/C, usearch11.0.667, 看不出来] - [2010.10, Bioinformatics] - Search and clustering orders of magnitude faster than BLAST
- [CD-HIT] - [Perl/C++, v4.8.1, 2019.3] [2012.10, Bioinformatics] - [CD-HIT: accelerated for clustering the next-generation sequencing data]