Well-supported phylogenies using largest subsets of core-genes by discrete particle swarm optimization
This work addresses the challenge of improving phylogenetic accuracy for plant species using genomic data, but it is incremental as it applies an existing optimization method to a specific biological domain.
The authors tackled the problem of constructing well-supported phylogenetic trees from core chloroplastic genes by identifying the largest subset of sequences, and they applied a discrete particle swarm optimization method to the Rosales order.
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.