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 language | English (US) |
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Article number | e63 |
Journal | Current Protocols in Microbiology |
Volume | 51 |
Issue number | 1 |
DOIs | |
State | Published - Nov 2018 |
Keywords
- evolution
- maximum likelihood
- phylogeny
- saturation
- virus
ASJC Scopus subject areas
- Parasitology
- Microbiology
- Virology