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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
36.1K
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
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.
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.
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