PMID- 21925283
OWN - NLM
STAT- MEDLINE
DCOM- 20120222
LR  - 20111107
IS  - 1095-9513 (Electronic)
IS  - 1055-7903 (Linking)
VI  - 61
IP  - 3
DP  - 2011 Dec
TI  - morePhyML: improving the phylogenetic tree space exploration with PhyML 3.
PG  - 944-8
LID - 10.1016/j.ympev.2011.08.029 [doi]
AB  - 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.
CI  - Copyright (c) 2011 Elsevier Inc. All rights reserved.
FAU - Criscuolo, Alexis
AU  - Criscuolo A
AD  - Unite de Biologie Moleculaire du Gene chez les Extremophiles, Departement de 
      Microbiologie, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France. 
      alexis.criscuolo@pasteur.fr
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20110908
PL  - United States
TA  - Mol Phylogenet Evol
JT  - Molecular phylogenetics and evolution
JID - 9304400
SB  - IM
MH  - Computational Biology/*methods
MH  - Likelihood Functions
MH  - *Phylogeny
MH  - *Software
MH  - Time Factors
EDAT- 2011/09/20 06:00
MHDA- 2012/02/23 06:00
CRDT- 2011/09/20 06:00
PHST- 2010/09/23 00:00 [received]
PHST- 2011/08/22 00:00 [revised]
PHST- 2011/08/31 00:00 [accepted]
PHST- 2011/09/20 06:00 [entrez]
PHST- 2011/09/20 06:00 [pubmed]
PHST- 2012/02/23 06:00 [medline]
AID - S1055-7903(11)00389-7 [pii]
AID - 10.1016/j.ympev.2011.08.029 [doi]
PST - ppublish
SO  - Mol Phylogenet Evol. 2011 Dec;61(3):944-8. doi: 10.1016/j.ympev.2011.08.029. Epub 
      2011 Sep 8.