Fast and robust multiple sequence alignment with phylogeny-aware gap placement

Abstract

Background: ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree.Results: This is achieved by incorporating a graph-based sequence representation combined with the advantages of the phylogeny-aware gap placement algorithm of Prank. Further, we account for variations in the substitution pattern by implementing context-specific profiles as in CS-Blast and by estimating amino acid frequencies from input data.Conclusions: ProGraphMSA shows good performance and competitive execution times in various benchmarks. © 2012 A M Szalkowski; licensee BioMed Central Ltd.