MergeAlign is a program that constructs a consensus multiple sequence alignment from multiple independent alignments. Using dynamic programming it efficiently combines individual multiple sequence alignments to generate a consensus that is maximally representative of all constituent alignments. Using MergeAlign to combine multiple sequence alignments generated using different matrices of amino acid substitution produces multiple sequence alignments that are more robust and more accurate than alignments generated using only a single matrix of amino acid substitution. Phylogenetic trees inferred from these MergeAlign alignments have better topological support values, are better resolved and show increased consistency. MergeAlign generates column support scores for each column in a multiple sequence alignment. When constituent alignments are generated using different models of amino acid substitution these support scores are related to alignment precision. MergeAlign can therefore be used to select accurately aligned data for downstream phylogenetic applications.

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