A multi-objective evolutionary approach to phylogenetic inference problems: Initial experiences porting PhyloMOEA to ParadisEO framework

Waldo Gonzalo Cancino Ticona (1) , Laetitia Jourdan (2) , El-Ghazali Talbi (2)

1 DOLPHIN - Parallel Cooperative Multi-criteria Optimization
2 LIFL - Laboratoire d'Informatique Fondamentale de Lille

Several phylogenetic reconstruction methods have been proposed in order to find the best tree that represents the evolutionary history of species analyzed. Most of these methods define an optimality criterion for the evaluation of possible solutions. However, different criteria may lead to dissimilar phylogenies, which often conflict with each other. In this context, a multi-objective approach can be useful since it could produce a set of optimal trees according to multiple criteria. PhyloMOEA proposes a multi objective approach to phylogenetic inference using maximum parsimony and maximum likelihood criteria. However, in many aspects, PhyloMOEA is a very basic tool with limited expandability. The availability of metaheuristic and bioinformatics reusable frameworks provides an excellent opportunity to increase PhyloMOEA capabilities. In this report we describe the development of a new parallel PhyloMOEA version using the ParadisEO framework.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Waldo Gonzalo Cancino Ticona, Laetitia Jourdan, El-Ghazali Talbi. A multi-objective evolutionary approach to phylogenetic inference problems: Initial experiences porting PhyloMOEA to ParadisEO framework. [Technical Report] RT-0366, INRIA. 2009. ⟨inria-00395336⟩