This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins.
Database search only
*Sequence type: protein or nucleotide
Pairwise alignment
*Sequence type: protein or nucleotide **Alignment type: local or global
Multiple sequence alignment
*Sequence type: protein or nucleotide. **Alignment type: local or global
Genomics analysis
*Sequence type: protein or nucleotide
Motif finding
*Sequence type: protein or nucleotide
Benchmarking
Alignment viewers, editors Please see List of alignment visualization software.
Short-read sequence alignment
See also List of open source bioinformatics software
References