期刊
MOLECULAR PHYLOGENETICS AND EVOLUTION
卷 61, 期 3, 页码 944-948出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2011.08.029
关键词
Phylogeny; Maximum Likelihood; PhyML; Tree search strategy; Local optimum; Ratchet
资金
- Agence Nationale de la Recherche (ANR) [07-JCJC-0094-01]
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. (C) 2011 Elsevier Inc. All rights reserved.
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