Pfaat (pronounced Pea-fat) is a Java application that allows one to edit, analyze, and annotate multiple sequence alignments. Annotations are a key feature, as they provide a framework for further sequence, structural and phylogenetic analysis.

References

PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments. Caffrey DR, Dana PH, Mathur V, Ocano M, Hong EJ, Wang YE, Somaroo S, Caffrey BE, Potluri S, Huang ES. 2007 Oct 11;8:381 PDF

Prediction of specificity-determining residues for small-molecule kinase inhibitors. Caffrey DR, Lunney EA, Moshinsky DJ. 2008 Nov 25;9:491 PDF