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New methods of identifying fast-evolving sites in aligned sequence data

Jermiin, L (CSIRO Ecosystem Sciences (CES))
Tuesday 21 June 2011, 16:50-17:10

Seminar Room 1, Newton Institute


Rate-heterogeneity across sites is a widely recognized problem in molecular phylogenetic studies. Attempts to overcome the problem involve deleting the fastest-evolving sites from the data before the phylogenetic analysis and/or using phylogenetic methods that assume rate-heterogeneity across sites can be modeled by a distribution of probabilities. Each of these methods has its advantages and limitations. Here, we describe and compare five metrics that may be used to identify the fast-evolving sites. One of these metrics (i.e., the probability of compatibility) turned out to be particular good at identifying fast-evolving sites, and when these sites are removed from the data, the result is an increase in the consistency of the alignment and, in some cases, another phylogeny.


[pdf ]


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