Close
Help





JOURNAL

Evolutionary Bioinformatics

Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny

Submit a Paper


Evolutionary Bioinformatics 2006:2 285-293

Published on 20 Feb 2007


Further metadata provided in PDF



Sign up for email alerts to receive notifications of new articles published in Evolutionary Bioinformatics

Tanja Gernhard1, Daniel Ford2, Rutger Vos3 and Mike Steel4

1Department of Mathematics, Kombinatorische Geometrie (M9), TU München, Boltzmannstr. 3, 85747 Garching, Germany. 2Department of Mathematics, Stanford University, U.S.A. 3Department of Biological Sciences, Simon Fraser University, Vancouver, Canada. 4Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.

Abstract: The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists– how can one assign relative dates to the vertices of the tree? In this paper we investigate this problem, assuming a uniform distribution on the order of the inner vertices of the tree (which includes, but is more general than, the popular Yule distribution on trees). We derive fast algorithms for computing the probability that (i) any given vertex in the tree was the j–th speciation event (for each j), and (ii) any one given vertex is earlier in the tree than a second given vertex. We show how the first algorithm can be used to calculate the expected length of any given interior edge in any given tree that has been generated under either a constant- rate speciation model, or the coalescent model.



Downloads

PDF  (689.36 KB PDF FORMAT)

RIS citation   (ENDNOTE, REFERENCE MANAGER, PROCITE, REFWORKS)

BibTex citation   (BIBDESK, LATEX)

XML





Quick Links


New article and journal news notification services