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Updated: Aug 14, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Protein phylogenetic inference using maximum likelihood with a genetic algorithm
1Department of Information and Computer Sciences, Faculty of Engineering Science, Osaka University, Japan.
Abstract:
This paper presents a method to construct phylogenetic trees from amino acid sequences. Our method uses a maximum likelihood approach which gives a confidence score for each possible alternative tree. Based on this approach, we developed a genetic algorithm for exploring the best score tree: randomly generated alternative trees are rearranged so that their scores are improved by utilizing crossover and mutation operators. In a test of our algorithm on a data set of EF-1 alpha sequences, we found that the performance of our algorithm is comparable to that of other tree-construction methods.
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