The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses

S. Nelesen, K. Liu, D. Zhao, C. R. Linder, Tandy Warnow

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Many multiple sequence alignment methods (MSAs) use guide trees in conjunction with a progressive alignment technique to generate a multiple sequence alignment but use differing techniques to produce the guide tree and to perform the progressive alignment. In this paper we explore the consequences of changing the guide tree used for the alignment routine. We evaluate four leading MSA methods (ProbCons, MAFFT, Muscle, and ClustalW) as well as a new MSA method (FTA, for "Fixed Tree Alignment") which we have developed, on a wide range of simulated datasets. Although improvements in alignment accuracy can be obtained by providing better guide trees, in general there is little effect on the "accuracy" (measured using the SP-score) of the alignment by improving the guide tree. However, RAxML-based phylogenetic analyses of alignments based upon better guide trees tend to be much more accurate. This impact is particularly significant for ProbCons, one of the best MSA methods currently available, and our method, FTA. Finally, for very good guide trees, phylogenies based upon FTA alignments are more accurate than phylogenies based upon ProbCons alignments, suggesting that further improvements in phylogenetic accuracy may be obtained through algorithms of this type.

Original languageEnglish (US)
Title of host publicationPacific Symposium on Biocomputing 2008, PSB 2008
Pages25-36
Number of pages12
StatePublished - Dec 1 2008
Event13th Pacific Symposium on Biocomputing, PSB 2008 - Kohala Coast, HI, United States
Duration: Jan 4 2008Jan 8 2008

Publication series

NamePacific Symposium on Biocomputing 2008, PSB 2008

Other

Other13th Pacific Symposium on Biocomputing, PSB 2008
CountryUnited States
CityKohala Coast, HI
Period1/4/081/8/08

Fingerprint

Sequence Alignment
Phylogeny
Muscle
Muscles

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • Medicine(all)

Cite this

Nelesen, S., Liu, K., Zhao, D., Linder, C. R., & Warnow, T. (2008). The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. In Pacific Symposium on Biocomputing 2008, PSB 2008 (pp. 25-36). (Pacific Symposium on Biocomputing 2008, PSB 2008).

The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. / Nelesen, S.; Liu, K.; Zhao, D.; Linder, C. R.; Warnow, Tandy.

Pacific Symposium on Biocomputing 2008, PSB 2008. 2008. p. 25-36 (Pacific Symposium on Biocomputing 2008, PSB 2008).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Nelesen, S, Liu, K, Zhao, D, Linder, CR & Warnow, T 2008, The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. in Pacific Symposium on Biocomputing 2008, PSB 2008. Pacific Symposium on Biocomputing 2008, PSB 2008, pp. 25-36, 13th Pacific Symposium on Biocomputing, PSB 2008, Kohala Coast, HI, United States, 1/4/08.
Nelesen S, Liu K, Zhao D, Linder CR, Warnow T. The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. In Pacific Symposium on Biocomputing 2008, PSB 2008. 2008. p. 25-36. (Pacific Symposium on Biocomputing 2008, PSB 2008).
Nelesen, S. ; Liu, K. ; Zhao, D. ; Linder, C. R. ; Warnow, Tandy. / The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. Pacific Symposium on Biocomputing 2008, PSB 2008. 2008. pp. 25-36 (Pacific Symposium on Biocomputing 2008, PSB 2008).
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