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A Novel Approach to Phylogenetic Tree Construction using Stochastic Optimization and Clustering

By Ling Qin, Yixin Chen, Yi Pan and Ling Chen

Abstract

Background: The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology. Results: A new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented. As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among the given objects. Conclusion: Our phylogenetic tree construction method is tested to compare its results with that of the genetic algorithm (GA). Experimental results show that our algorithm converges much faster and also achieves higher quality than GA

Topics: genetic algorithms, phylogeny, proteins, algorithms, biology, phylogenetic tree construction method, Bioinformatics, Computer Sciences, Ecology and Evolutionary Biology
Publisher: ScholarWorks @ Georgia State University
Year: 2006
OAI identifier: oai:scholarworks.gsu.edu:computer_science_facpub-1012

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