title: MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.
abstract: BACKGROUND
  Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate multiple alignments is still a challenge.
  
  
  RESULTS
  We present MSAProbs, 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. Furthermore, two critical bioinformatics techniques, namely weighted probabilistic consistency transformation and weighted profile-profile alignment, are incorporated to improve alignment accuracy. 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.
  
  
  BACKGROUND
  The source code of MSAProbs, written in C++, is freely and publicly available from http://msaprobs.sourceforge.net.
authors.affiliation: School of Computer Engineering, Nanyang Technological University, Singapore. liuy0039@ntu.edu.sg
authors.forename: Yongchao
authors.initials: Y
authors.lastname: Liu
authors.forename: Bertil
authors.initials: B
authors.lastname: Schmidt
authors.forename: Douglas L
authors.initials: DL
authors.lastname: Maskell
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D008390:Markov Chains; D011336:Probability; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software