Fast and robust multiple sequence alignment with phylogeny-aware gap placement
<p>Abstract</p> <p>Background</p> <p>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...
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| Format: | Article |
| Language: | English |
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BMC
2012-06-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/13/129 |
| Summary: | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>ProGraphMSA shows good performance and competitive execution times in various benchmarks.</p> |
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| ISSN: | 1471-2105 |