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:Alignment type: local or global

Multiple sequence alignment

Sequence type: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