Phylogenetic tree reconstruction using self-adaptive genetic algorithm

Abstract

We developed a self-adaptive genetic algorithm for a maximum likelihood reconstruction of phylogenetic trees using nucleotide sequence data. It resulted in a faster reconstruction of the trees with less computing power arid automatic self-adjustment of settings of the optimization algorithm parameters. We focused on the use of genetic algorithms (GAS) with self-adaptive control parameters arid GAS integration with phvlogenetic tree representations. The developed technique is applicable to any nucleotide sequences inferring evolutionary relationships of organisms.

Introduction to Pattern Recognition and Bioinformatics

“…To explain the evolutionary history of today's species and how species relate to one another in terms of common ancestors, trees are constructed whose leaves represent the present-day species and intermediate nodes represent the hypothesized ancestors. These kind of labeled binary trees are called phylogenetic trees [163,186,191,218,308,315]. Phylogenetic analysis is used to study the evolutionary relationship.…”

“…Given data for a set of objects, the phylogenetic tree reconstruction problem is to find the particular permutation of objects that optimize the given criteria. A number of algorithms are available to solve this problem [218,308,315]. …”

The AxML program family for maximum likelihood‐based phylogenetic tree inference

“…Parallel implementations are available for the following sequential programs: DNAml [16], fastDNAml [4], treepuzzle [17]. As alternative to the above approaches, sequential and parallel implementations of genetic algorithms for maximum likelihood-based phylogenetic tree inference have been proposed, for example in [5,18].…”

Evolutionary computation in bioinformatics: a review

“…The only difference with TSP is that the end points of the chromosome GA are relevant in phylogenetic trees as they represent the starting and the end points of evolutionary relationship. GAs has also been used [58] for automatic self-adjustment of the parameters of the optimization algorithm of phylogenetic trees.…”