Well-supported phylogenies using largest subsets of core-genes by discrete particle swarm optimization

Reem Alsrraj, Bassam AlKindy, Christophe Guyeux, Laurent Philippe, Jean-François Couchot

The number of complete chloroplastic genomes increases day after day, making it possible to rethink plants phylogeny at the biomolecular era. Given a set of close plants sharing in the order of one hundred of core chloroplastic genes, this article focuses on how to extract the largest subset of sequences in order to obtain the most supported species tree. Due to computational complexity, a discrete and distributed Particle Swarm Optimization (DPSO) is proposed. It is finally applied to the core genes of Rosales order.

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