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SUMMARY:An empirical study of the effect of sequence alignment on phylogen
 etic analysis - Blackburne\, B (Manchester)
DTSTART:20110622T140000Z
DTEND:20110622T142000Z
UID:TALK31828@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Phylogenetic analyses start with a multiple sequence alignment
 \, which is often accepted as known despite wide recognition that errors m
 ay impact downstream phylogenetic analysis. Many phylogenetic methods invo
 lve testing which of a range of competing hypotheses best describe the evo
 lution of a set of sequences. These tests may be justified statistically w
 hen using the correct alignment\, but errors in the alignment lead to non-
 homologous characters being placed together\, which in turn may systematic
 ally bias the test. We investigate empirically the impact of different ali
 gnment methods on phylogenetic analyses and assess the relative impact of 
 different approximations used by different alignment methods.\n\nWe examin
 e the effect of alignment on two phylogenetic analyses that are commonly u
 sed in computational biology: the inference of a maximum-likelihood tree u
 sing RAxML\, and a test for positive selection by comparing the M7 and M8 
 models in PAML. We test 200 sets of sequences from the Adaptive Evolution 
 Database using the popular aligners ClustalW\, Muscle\, MAAFT\, ProbCons\,
  and the phylogenetic aligner Prank. We also sample from the posterior dis
 tribution of the statistical aligner BAli-Phy\, which enables us to compar
 e the relative impact of aligner choice to uncertainty from a single align
 er.\n\nThe algorithmic basis of an aligner tends to determine the outcome 
 of the phylogenetic analysis. For example\, trees estimated from progressi
 ve aligners tend to be more similar to one another than those estimated fr
 om phylogenetically aware (Prank) or consensus (ProbCons) aligners. Moreov
 er the spread of phylogenetic parameter estimates inferred from BAli-Phys 
 posterior distribution of alignments is much smaller than the differences 
 between other aligners\, suggesting differences are larger than could be e
 xpected by chance. Of the aligners examined\, our results suggest that the
  phylogenetically informed Prank provides the closest approximation to ful
 l statistical alignment.\n
LOCATION:Seminar Room 1\, Newton Institute
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