Building (Viral) Phylogenetic Trees Using a Maximum Likelihood Approach

Kelly M. King, Koenraad Van Doorslaer

Research output: Contribution to journalArticle

Abstract

Phylogenetic analyses allow for inferring a hypothesis about the evolutionary history of a set of homologous molecular sequences. This hypothesis can be used as the basis for further molecular and computational studies. In this unit, we offer one specific method to construct a Maximum Likelihood phylogenetic tree. We outline how to identify homologous sequences and construct a multiple sequence alignment. Following alignment, sequences are screened for potentially confounding factors such as recombination and genetic saturation. Finally, a Maximum Likelihood phylogenetic tree can be constructed implementing a rigorously tested model of evolution. The workflow outlined in this unit provides sufficient background for inferring a robust phylogenetic tree starting from a particular gene of interest.

Original languageEnglish (US)
Article numbere63
JournalCurrent Protocols in Microbiology
Volume51
Issue number1
DOIs
StatePublished - Nov 2018

Keywords

  • evolution
  • maximum likelihood
  • phylogeny
  • saturation
  • virus

ASJC Scopus subject areas

  • Parasitology
  • Microbiology
  • Virology

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