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

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

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.

[1] Riccardo Poli,et al. Particle swarm optimization , 1995, Swarm Intelligence.

[2] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[3] Robert K. Jansen,et al. Automatic annotation of organellar genomes with DOGMA , 2004, Bioinform..

[4] Masami Hasegawa,et al. CONSEL: for assessing the confidence of phylogenetic tree selection , 2001, Bioinform..

[5] Jacques M. Bahi,et al. Finding the Core-Genes of Chloroplasts , 2014, ArXiv.

[6] Eric C. Rouchka,et al. Review of Phylogenetic Tree Construction , 2007 .

[7] Jacques M. Bahi,et al. Gene similarity-based approaches for determining core-genes of chloroplasts , 2014, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[8] Jacques M. Bahi,et al. Hybrid Genetic Algorithm and Lasso Test Approach for Inferring Well Supported Phylogenetic Trees Based on Subsets of Chloroplastic Core Genes , 2015, AlCoB.