Phylogenetic model evaluation

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

Research output: Chapter in Book/Report/Conference proceedingChapter

35 Citations (Scopus)

Abstract

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
Title of host publicationBioinformatics
Subtitle of host publicationData, Sequence Analysis and Evolution
PublisherHumana Press
Pages331-364
Number of pages34
Volume452
ISBN (Print)9781588297075
DOIs
Publication statusPublished - 2008

Publication series

NameMethods in Molecular Biology
Volume452
ISSN (Print)1064-3745

Keywords

  • Evolutionary processes
  • Markov models
  • Model evaluation
  • Model selection
  • Phylogenetic assumptions

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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