Phylogenetic Tree Construction Using Chemical Reaction Optimization
Phylogenetic tree construction (PT) problem is a well-known NP-hard optimization problem that finds most accurate tree representing evolutionary relationships among species. Different criteria are used to measure the quality of a phylogeny tree by analyzing their relationships and nucleotide sequences. With increasing number of species, solution space of phylogenetic tree construction problem grows exponentially. In this paper, we have implemented Chemical Reaction Optimization algorithm to solve phylogeny construction problem for multiple datasets. For exploring both local and global search space, we have redesigned four elementary operators of CRO to solve phylogeny construction problem. One correction method has been designed for finding good combination of species according to maximum parsimony criterion. The experimental results show that for maximum parsimony criterion our implemented algorithm gives better results for three real datasets and same for one dataset.
KeywordsPhylogenetic tree Maximum parsimony Metaheuristics Chemical Reaction Optimization
- 2.Stamatakis, A.: Phylogenetics: applications, software and challenges. Cancer Genomics-Proteomics 2(5), 301–305 (2005)Google Scholar
- 6.Felsenstein, J.: PHYLIP (phylogeny inference package), version 3.5 c (1993)Google Scholar
- 10.Zwickl, D.J.: Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion (2006)Google Scholar