Evolving Phylogenetic Trees: An Alternative to Black-Box Approaches

Oclair PradoFernando J. Von ZubenSérgio F. dos Reis

This paper presents the main steps to reconstruct phylogenetic trees using an evolutionary algorithm with a wide range of alternative computational procedures for fitness evaluation and for tuning the search engine. Due to the fine equilibrium between exploration and exploitation of the search space, high-quality reconstructions are obtained among an explosion of candidates and with the additional requirement of adjusting the length of all branches in a given tree. A toolbox is available, and the matrix codification adopted, the associated genetic operators, and the optimization procedures involved are clearly described to guarantee reproducibility.

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