Bob Edgar's Multiple Sequence Alignment tool is available here. This module produces either FASTA multiple alignment format or ClustalW multiple alignment format which is parseable through Bio::AlignIO.
- Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004 Aug 19;5:113. DOI:10.1186/1471-2105-5-113 |
- Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-7. DOI:10.1093/nar/gkh340 |