MergeAlign is a program that constructs a consensus multiple sequence alignment from multiple different alignments of the same sets of sequences. In doing so it improves the accuracy of the alignment over any single method and provides insight into which positions in the alignment are well-aligned and which positions are not.

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 applications.

Download a command line executable version of MergeAlign below

Download the 91 MergeAlign matrices below

If you use MergeAlign in your work please cite:

Collingridge, P. and Kelly, S. (2012). MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. BMC Bioinformatics (13) 1, 117.