Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences. It uses probabilistic modeling and consistenct-based technigues in the alignment construction. The Authors claim this tool to have improved alignments compared to T-Coffee, Clustal W, and Dialign.
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S "ProbCons: Probabilistic consistency-based multiple sequence alignment" Genome Res. 2005 Feb;15(2):330-40. https://doi.org/10.1101/gr.2821705
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