SeqAn

SeqAn seqan2007 is an open-source C++ library of biological sequence analysis algorithms, including sequence IO, pairwise and multiple sequence alignment, and graph algorithms. No interface currently exists between SeqAn and BioPerl, though developing one might be a useful (and easily maintainable) replacement for some of the older BioPerl XS-based alignment implementations.

References

<biblio>

1. seqan2007 pmid=18184432

</biblio>