List of sequence alignment software

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

Alignment viewers, editors
Please see List of alignment visualization software.