Abstract
BackgroundProGraphMSA 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.ResultsThis 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.ConclusionsProGraphMSA shows good performance and competitive execution times in various benchmarks.
Highlights
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 tool includes methods like progressive partial order alignment [2] combined with phylogeny-aware gap placement [3], which causes the gaps in the multiple sequence alignment to principally follow the branching pattern of the guide tree, but still allows for exceptions to account for alternative splicings and errors in the guide tree
Model of evolution Unlike in the progressive partial order alignment algorithm [14], we model the evolution of indels using a pair-Hidden Markov Model (HMM) (Figure 2), which is used at each internal node of the guide tree for the alignment of the graphs representing the ancestral sequences of the left and right sub-trees
Summary
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
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