title: morePhyML: improving the phylogenetic tree space exploration with PhyML 3.
abstract: PhyML is a widely used Maximum Likelihood (ML) phylogenetic tree inference software based on a standard hill-climbing method. Starting from an initial tree, the version 3 of PhyML explores the tree space by using "Nearest Neighbor Interchange" (NNI) or "Subtree Pruning and Regrafting" (SPR) tree swapping techniques in order to find the ML phylogenetic tree. NNI-based local searches are fast but can often get trapped in local optima, whereas it is expected that the larger (but slower to cover) SPR-based neighborhoods will lead to trees with higher likelihood. Here, I verify that PhyML infers more likely trees with SPRs than with NNIs in almost all cases. However, I also show that the SPR-based local search of PhyML often does not succeed at locating the ML tree. To improve the tree space exploration, I deliver a script, named morePhyML, which allows escaping from local optima by performing character reweighting. This ML tree search strategy, named ratchet, often leads to higher likelihood estimates. Based on the analysis of a large number of amino acid and nucleotide data, I show that morePhyML allows inferring more accurate phylogenetic trees than several other recently developed ML tree inference softwares in many cases.
authors.affiliation: Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France. alexis.criscuolo@pasteur.fr
authors.forename: Alexis
authors.initials: A
authors.lastname: Criscuolo
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016013:Likelihood Functions; D010802:Phylogeny; D012984:Software; D013997:Time Factors