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

Building (Viral) Phylogenetic Trees Using a Maximum Likelihood Approach.

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School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona.
Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, BIO5 Institute, and the University of Arizona Cancer Center, University of Arizona, Tucson, Arizona.


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.


evolution; maximum likelihood; phylogeny; saturation; virus

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