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

Kelly M King1, Koenraad Van Doorslaer1,2

  • 1School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona.

Current Protocols in Microbiology
|September 29, 2018
PubMed
Summary

This study presents a Maximum Likelihood method for constructing phylogenetic trees from molecular sequences. It details steps for sequence alignment and analysis, enabling robust evolutionary history inference.

Keywords:
evolutionmaximum likelihoodphylogenysaturationvirus

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic analyses are crucial for hypothesizing evolutionary history from homologous molecular sequences.
  • These hypotheses form the foundation for subsequent molecular and computational research.

Purpose of the Study:

  • To present a specific method for constructing a Maximum Likelihood phylogenetic tree.
  • To provide a comprehensive workflow for inferring evolutionary history from gene sequences.

Main Methods:

  • Identification of homologous sequences and construction of multiple sequence alignment.
  • Screening of aligned sequences for recombination and genetic saturation.
  • Construction of a Maximum Likelihood phylogenetic tree using a rigorously tested evolutionary model.

Main Results:

  • A detailed workflow for inferring phylogenetic trees is outlined.
  • The method ensures robustness by addressing potential confounding factors in sequence data.

Conclusions:

  • The presented workflow enables the inference of a robust phylogenetic tree from a gene of interest.
  • This method serves as a valuable resource for molecular and computational studies in evolutionary biology.