Stack Based Fitness Evaluation for Phylogenetic Tree Reconstruction Using Genetic Algorithm

The problem considered is the estimation of the evolutionary history of a collection of organisms in terms of a phylogenetic tree using genetic algorithm. This paper presents a new chromosome representation scheme for individuals in the population. A new stack based fitness evaluation method has been proposed to handle the populations generated in genetic algorithms. The problem of phylogenetic tree reconstruction is a hard combinatorial optimization problem for which different Evolutionary Algorithmic approaches are proposed and evaluated. It is shown that Genetic Algorithm for phylogenetic tree reconstruction by maximum parsimony method with the proposed stack based fitness evaluation scheme and with appropriate individual representation scheme performs well with reasonable storage space and increased computational speed.