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                                  ---  PhyML 20120412  ---                                             
                            http://www.atgc-montpellier.fr/phyml                                          
                         Copyright CNRS - Universite Montpellier II                                 
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. Sequence filename: 			polymorphisms_move.phy
. Data set: 				#1
. Tree topology search : 		NNIs
. Initial tree: 			BioNJ
. Model of nucleotides substitution: 	GTR
. Number of taxa: 			12
. Log-likelihood: 			-478403.36249
. Unconstrained likelihood: 		-452917.11254
. Parsimony: 				46122
. Tree size: 				0.34587
. Discrete gamma model: 		Yes
  - Number of categories: 		4
  - Gamma shape parameter: 		0.014
. Nucleotides frequencies:
  - f(A)= 0.19734
  - f(C)= 0.30466
  - f(G)= 0.30755
  - f(T)= 0.19045
. GTR relative rate parameters : 
  A <-> C    0.88408
  A <-> G    7.98444
  A <-> T    0.86873
  C <-> G    4.85179
  C <-> T    9.08975
  G <-> T    1.00000

. Instantaneous rate matrix : 
  [A---------C---------G---------T------]
  -0.89710   0.08360   0.76215   0.05135  
   0.05415  -1.05457   0.46313   0.53729  
   0.48902   0.45878  -1.00691   0.05911  
   0.05321   0.85951   0.09545  -1.00817  



. Run ID:				none
. Random seed:				500245
. Subtree patterns aliasing:		no
. Version:				20120412
. Time used:				0h0m36s (36 seconds)

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 Suggested citations:
 S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
 "New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
 Systematic Biology. 2010. 59(3):307-321.

 S. Guindon & O. Gascuel
 "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
 Systematic Biology. 2003. 52(5):696-704.
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