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

Adam M Szalkowski

Author affiliations

Department of Computer Science, ETH Zürich, Universitätstrasse, Switzerland

Swiss Institute of Bioinformatics, Switzerland

Citation and License

BMC Bioinformatics 2012, 13:129  doi:10.1186/1471-2105-13-129

Published: 13 June 2012



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.


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.


ProGraphMSA shows good performance and competitive execution times in various benchmarks.