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This list of sequence alignment software is a compilation of software tools and web portals used in pairwise
sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Alig ...
and
multiple sequence alignment Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutio ...
. See
structural alignment software This list of structural comparison and alignment software is a compilation of software tools and web portals used in pairwise or multiple structural comparison A structure is an arrangement and organization of interrelated elements in a material ...
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 This is a list of computer software which is made for bioinformatics and released under open-source software licenses with articles in Wikipedia. See also * List of sequence alignment software * List of open-source healthcare software * List o ...


References

{{Reflist
Sequence In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is calle ...
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 searc ...