General heterotachy and distance method adjustments.

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General heterotachy and distance method adjustments.

Mol Biol Evol. 2009 Dec;26(12):2689-97

Authors: Wu J, Susko E

Abstract
Heterotachy is a general term to describe positions in a sequence that evolve at different rates in different lineages. Kolaczkowski and Thornton (2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.) recently described an intriguing heterotachy model that leads to topological bias for likelihood-based methods and parsimony methods. In this article, we show that heterotachy can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each site. Motivated by this idea, we propose a pairwise alpha heterotachy adjustment model, which gives us much improved topological estimation in the settings by Kolaczkowski and Thornton (2004).

PMID: 19687305 [PubMed - indexed for MEDLINE]