title: PnpProbs: a better multiple sequence alignment tool by better handling of guide trees.
abstract: BACKGROUND
  This paper describes a new MSA tool called PnpProbs, which constructs better multiple sequence alignments by better handling of guide trees. It classifies sequences into two types: normally related and distantly related. For normally related sequences, it uses an adaptive approach to construct the guide tree needed for progressive alignment; it first estimates the input's discrepancy by computing the standard deviation of their percent identities, and based on this estimate, it chooses the better method to construct the guide tree. For distantly related sequences, PnpProbs abandons the guide tree and uses instead some non-progressive alignment method to generate the alignment.
  
  
  RESULTS
  To evaluate PnpProbs, we have compared it with thirteen other popular MSA tools, and PnpProbs has the best alignment scores in all but one test. We have also used it for phylogenetic analysis, and found that the phylogenetic trees constructed from PnpProbs' alignments are closest to the model trees.
  
  
  CONCLUSIONS
  By combining the strength of the progressive and non-progressive alignment methods, we have developed an MSA tool called PnpProbs. We have compared PnpProbs with thirteen other popular MSA tools and our results showed that our tool usually constructed the best alignments.
authors: HKU-BGI Bioinformatics Algorithms & Core Technology Research Lab, Computer Science Department, University of Hong Kong, Hong Kong, China.
authors: Yongtao
authors: Y
authors: Ye
authors: HKU-BGI Bioinformatics Algorithms & Core Technology Research Lab, Computer Science Department, University of Hong Kong, Hong Kong, China.
authors: Tak-Wah
authors: TW
authors: Lam
authors: HKU-BGI Bioinformatics Algorithms & Core Technology Research Lab, Computer Science Department, University of Hong Kong, Hong Kong, China. hfting@cs.hku.hk.
authors: Hing-Fung
authors: HF
authors: Ting
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D030562:Databases, Protein; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D013997:Time Factors
keywords: Guide trees; Multiple sequence alignment; Phylogenetic trees