Multiple protein sequence alignment with MSAProbs

Methods Mol Biol. 2014;1079:211-8. doi: 10.1007/978-1-62703-646-7_14.


Multiple sequence alignment (MSA) generally constitutes the foundation of many bioinformatics studies involving functional, structural, and evolutionary relationship analysis between sequences. As a result of the exponential computational complexity of the exact approach to producing optimal multiple alignments, the majority of state-of-the-art MSA algorithms are designed based on the progressive alignment heuristic. In this chapter, we outline MSAProbs, a parallelized MSA algorithm for protein sequences based on progressive alignment. To achieve high alignment accuracy, this algorithm employs a hybrid combination of a pair hidden Markov model and a partition function to calculate posterior probabilities. Furthermore, we provide some practical advice on the usage of the algorithm.

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Markov Chains
  • Proteins / chemistry*
  • Sequence Alignment / methods*
  • Software*


  • Proteins