Identifying optimal models of evolution

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

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

13 Citations (Scopus)


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.
Number of pages42
Publication statusPublished - 2017
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • 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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