Phylogenetic model evaluation.

Lars Sommer Jermiin*, Vivek Jayaswal, Faisal Ababneh, John Robinson

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review


Most phylogenetic methods are model-based and depend on Markov models designed to approximate the evolutionary rates between nucleotides or amino acids. When Markov models are selected for analysis of alignments of these characters, it is assumed that they are close approximations of the evolutionary processes that gave rise to the data. A variety of methods have been developed for estimating the fit of Markov models, and some of these methods are now frequently used for the selection of Markov models. In a growing number of cases, however, it appears that the investigators have used the model-selection methods without acknowledging their inherent shortcomings. This chapter reviews the issue of model selection and model evaluation.

Original languageEnglish
Pages (from-to)331-364
Number of pages34
JournalMethods in molecular biology (Clifton, N.J.)
Publication statusPublished - 2008

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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