Dataset Information
Fast and robust multiple sequence alignment with phylogeny-aware gap placement.
Ontology highlight
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.
SUBMITTER: Szalkowski AM
PROVIDER: S-EPMC3495709 | biostudies-literature | 2012 Jun
REPOSITORIES: biostudies-literature
Publications
Fast and robust multiple sequence alignment with phylogeny-aware gap placement.
BMC bioinformatics 20120613
<h4>Background</h4>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.<h4>Results</h4>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 imp ...[more]