Building (Viral) Phylogenetic Trees Using a Maximum Likelihood Approach

Curr Protoc Microbiol. 2018 Nov;51(1):e63. doi: 10.1002/cpmc.63. Epub 2018 Sep 28.


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. © 2018 by John Wiley & Sons, Inc.

Keywords: evolution; maximum likelihood; phylogeny; saturation; virus.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / methods*
  • Phylogeny*
  • Viruses / classification*
  • Viruses / genetics*