alignment.phy_phyml_stats.txt

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                                  ---  PhyML 20120412  ---                                             
                            http://www.atgc-montpellier.fr/phyml                                          
                         Copyright CNRS - Universite Montpellier II                                 
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. Sequence filename: 			alignment.phy
. Data set: 				#1
. Tree topology search : 		NNIs
. Initial tree: 			BioNJ
. Model of nucleotides substitution: 	GTR
. Number of taxa: 			52
. Log-likelihood: 			-9632.95744
. Unconstrained likelihood: 		-7409.76327
. Parsimony: 				1416
. Tree size: 				1.02196
. Discrete gamma model: 		Yes
  - Number of categories: 		4
  - Gamma shape parameter: 		0.414
. Nucleotides frequencies:
  - f(A)= 0.29383
  - f(C)= 0.23312
  - f(G)= 0.22011
  - f(T)= 0.25295
. GTR relative rate parameters : 
  A <-> C    1.50280
  A <-> G   12.52152
  A <-> T    1.13675
  C <-> G    0.29287
  C <-> T   17.10083
  G <-> T    1.00000

. Instantaneous rate matrix : 
  [A---------C---------G---------T------]
  -0.81730   0.08436   0.66369   0.06924  
   0.10633  -1.16351   0.01552   1.04165  
   0.88598   0.01644  -0.96333   0.06091  
   0.08043   0.96000   0.05300  -1.09344  



. Run ID:				none
. Random seed:				1746899585
. Subtree patterns aliasing:		no
. Version:				20120412
. Time used:				0h0m51s (51 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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