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A tool for multiple sequence alignment (MSA) for protein sequences. Features: uses a combination of hidden Markov models and partition functions, weighted probabilistic consistency transformation, weighted profile to profile alignments. The Authors claim MSAprobs to have better accuracy than ClustalW, MAFFT, MUSCLE, ProbCons, and Probalign. A multicore version is available. See "LINKS."


Sequence analysis


  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Software interface: command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Apache Software License;GNU General Public License version v2
  • Cost: Free
  • Version name: 0.9.7
  • Credit: -
  • Contact: Yongchao Liu liuy0039 _at_
  • Collection: -


Yongchao Liu, Bertil Schmidt, Douglas L Maskell "MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities" Bioinformatics, Volume 26, Issue 16, 15 August 2010, Pages 1958–1964
PMID: 20576627

Liu Y, Schmidt B "Multiple protein sequence alignment with MSAProbs." Methods Mol Biol. 2014;1079:211-8.
PMID: 24170405

Download and documentation

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