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

<small><nowiki>*</nowiki>Sequence type: protein or nucleotide</small>

Pairwise alignment

<small><nowiki>*</nowiki>Sequence type: protein or nucleotide <nowiki>**</nowiki>Alignment type: local or global</small>

Multiple sequence alignment

<small><nowiki>*</nowiki>Sequence type: protein or nucleotide. <nowiki>**</nowiki>Alignment type: local or global</small>

Genomics analysis

<small><nowiki>*</nowiki>Sequence type: protein or nucleotide</small> <br/>

Motif finding

<small><nowiki>*</nowiki>Sequence type: protein or nucleotide</small> <br/>

Benchmarking

Alignment viewers, editors

Please see List of alignment visualization software.

Short-read sequence alignment

See also

• List of open source bioinformatics software

References