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CATEGORIES:rern2's list
SUMMARY:New methods of detecting violated phylogenetic ass
 umptions: Implications on comparative genomics - L
 ars Jermiin\, University of Sydney
DTSTART;TZID=Europe/London:20070831T110000
DTEND;TZID=Europe/London:20070831T120000
UID:TALK7903AThttp://talks.cam.ac.uk
URL:http://talks.cam.ac.uk/talk/index/7903
DESCRIPTION:Most phylogenetic methods assume that the sequence
 s of nucleotides or amino acids have evolved under
  stationary\, reversible and homogeneous condition
 s. When these assumptions are violated by the data
 \, as would be the case if there is compositional 
 heterogeneity across the sequences\, the phylogene
 tic estimates are obtained under an incorrect mode
 l and thus subject to error. Methods to examine al
 igned sequences for violation of these assumptions
  have been available for years\, but they are rare
 ly used\, presumably because they are not widely k
 nown or because they are poorly understood. Here w
 e describe and compare matched-pairs tests for sym
 metry of two-dimensional contingency tables from h
 omologous sequences and show that the tests of sym
 metry\, marginal symmetry and internal symmetry ca
 n be used not only to detect violation of the assu
 mption of stationarity\, reversibility and homogen
 eity\, but also to identify what may underpin this
  violation. Under the assumption that the sequence
 s evolved under stationary\, reversible and homoge
 neous conditions\, the tests are unaffected by inv
 ariant sites and divergence between the pairs of s
 equences\, implying that they may be used to ident
 ify suitable substitution models for estimation of
  evolutionary relationships under a Markovian mode
 l.
LOCATION:Semiar Room\, Department of Biochemistry\, Hopkins
  Building (old building)
CONTACT:Dr Ellen Nisbet
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