PROBCONS is an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.
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Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005.
PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment.
Genome Research 15: 330-340.