MMSA is a novel MPSA (Alignment of protein sequences) program based on the SeqAn sequence alignment library. It has a strict modular structure, which allows to swap different components of the alignment process and, thus, to investigate their contribution to the alignment quality. The program can be used to see how alignment quality changes depending on the input information, guiding trees, the applied consistency transformations, and the strategy for iterative refinement during post-processing.
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BMC Bioinformatics. 2012 Apr 29;13:64. doi: 10.1186/1471-2105-13-64.
Comprehensive comparison of graph based multiple protein sequence alignment strategies.
Plyusnin I1, Holm L.