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                                  ---  PhyML 3.3.20211231  ---                                             
                              http://www.atgc-montpellier.fr/phyml                                          
                             Copyright CNRS - Universite Montpellier                                 
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. Sequence filename: 			raytAln.phy
. Data set: 				#1
. Initial tree: 			BioNJ
. Model of nucleotides substitution: 	GTR
. Number of taxa: 			138
. Log-likelihood: 			-12653.70432
. Unconstrained log-likelihood: 	-2758.11258
. Composite log-likelihood: 		-90480.93534
. Parsimony: 				2744
. Tree size: 				9.48533
. Discrete gamma model: 		Yes
  - Number of classes: 			4
  - Gamma shape parameter: 		0.737
  - Relative rate in class 1: 		0.08207 [freq=0.250000] 		
  - Relative rate in class 2: 		0.38040 [freq=0.250000] 		
  - Relative rate in class 3: 		0.93779 [freq=0.250000] 		
  - Relative rate in class 4: 		2.59975 [freq=0.250000] 		
. Nucleotides frequencies:
  - f(A)=  0.18381
  - f(C)=  0.30992
  - f(G)=  0.30238
  - f(T)=  0.20388
. GTR relative rate parameters :
  A <-> C    1.31888
  A <-> G    3.76931
  A <-> T    1.17611
  C <-> G    1.14299
  C <-> T    3.75144
  G <-> T    1.00000
. Instantaneous rate matrix : 
  [A---------C---------G---------T------]
  -1.21731   0.27824   0.77584   0.16323  
   0.16502  -0.92093   0.23526   0.52065  
   0.47163   0.24113  -0.85155   0.13879  
   0.14716   0.79144   0.20583  -1.14443  


. Run ID:				none
. Random seed:				1662482029
. Subtree patterns aliasing:		no
. Version:				3.3.20211231
. Time used:				0h1m45s (105 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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