Identifying optimal models of evolution

Lars S. Jermiin, Vivek Jayaswal, Faisal M. Ababneh, John Robinson

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Abstract

Most phylogenetic methods are model-based and depend on models of evolution designed to approximate the evolutionary processes. Several methods have been developed to identify suitable models of evolution for phylogenetic analysis of alignments of nucleotide or amino acid sequences and some of these methods are now firmly embedded in the phylogenetic protocol. However, in a disturbingly large number of cases, it appears that these models were used without acknowledgement of their inherent shortcomings. In this chapter, we discuss the problem of model selection and show how some of the inherent shortcomings may be identified and overcome.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages379-420
Number of pages42
Volume1525
DOIs
Publication statusPublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1525
ISSN (Print)1064-3745

Keywords

  • Evolutionary processes
  • Homogeneous conditions
  • Markov models
  • Model evaluation
  • Model selection
  • Phylogenetic assumptions
  • Rate-heterogeneity across sites
  • Reversible conditions
  • Stationary conditions

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Jermiin, L. S., Jayaswal, V., Ababneh, F. M., & Robinson, J. (2017). Identifying optimal models of evolution. In Methods in Molecular Biology (Vol. 1525, pp. 379-420). (Methods in Molecular Biology; Vol. 1525). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-6622-6_15