Optimizing the Order of Taxon Addition in Phylogenetic Tree Construction Using Genetic Algorithm

Yong-Hyuk Kim¹, Seung-Kyu Lee², and Byung-Ro Moon¹

¹School of Computer Science & Engineering
Seoul National University
Shilim-dong, Kwanak-gu
Seoul, 151-742 Korea
{yhdfly,moon}@soar.snu.ac.kr

²NHN Corp.
7th floor, Startower
737 Yoksam-dong, Kangnam-gu
Seoul, Korea
spin30@soar.snu.ac.kr

Abstract. Phylogenetics has gained in public favor for the analysis of DNA sequence data as molecular biology has advanced. Among a number of algorithms for phylogenetics, the fastDNAml is considered to have reasonable computational cost and performance. However, it has a defect that its performance is likely to be significantly affected by the order of taxon addition. In this paper, we propose a genetic algorithm for optimizing the order of taxon addition in the fastDNAml. Experimental results show that the fastDNAml with the optimized order of taxon addition constructs more probable evolutionary trees in terms of the maximum likelihood.

LNCS 2724, p. 2168 ff.

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