Authors:
Karla E. Vazquez-Ortiz
;
Jean-Michel Richer
and
David Lesaint
Affiliation:
University of Angers, France
Keyword(s):
Phylogenetic Reconstruction, Maximum Parsimony, GPU, Simulated Annealing, Path-relinking.
Related
Ontology
Subjects/Areas/Topics:
Agents
;
Algorithms and Software Tools
;
Artificial Intelligence
;
Bioinformatics
;
Biomedical Engineering
;
Enterprise Information Systems
;
Information Systems Analysis and Specification
;
Methodologies and Technologies
;
Operational Research
;
Simulation
Abstract:
The phylogenetic reconstruction is considered a central underpinning of diverse field of biology like: ecology, molecular biology and physiology. The main example is modeling patterns and processes of evolution. Maximum Parsimony (MP) is an important approach to solve the phylogenetic reconstruction by minimizing the total number of genetic transformations, under this approach different metaheuristics have been implemented like tabu search, genetic and memetic algorithms to cope with the combinatorial nature of the problem. In this paper we review different strategies that could be added to existing implementations to improve their efficiency and accuracy. First we present two different techniques to evaluate the objective function by using CPU and GPU technology, then we show a Path-Relinking implementation to compare tree topologies and finally we introduces the application of these techniques in a Simulated Annealing algorithm looking for an optimal solution.