MSAProbs is a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners.
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Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
“MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities“.
Bioinformatics, 2010, 26(16): 1958 -1964