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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: 			311
. Log-likelihood: 			-2243.78424
. Unconstrained log-likelihood: 	-2279.76552
. Composite log-likelihood: 		-245892.45510
. Parsimony: 				362
. Tree size: 				1.46413
. Discrete gamma model: 		Yes
  - Number of classes: 			4
  - Gamma shape parameter: 		0.759
  - Relative rate in class 1: 		0.08680 [freq=0.250000] 		
  - Relative rate in class 2: 		0.39006 [freq=0.250000] 		
  - Relative rate in class 3: 		0.94490 [freq=0.250000] 		
  - Relative rate in class 4: 		2.57824 [freq=0.250000] 		
. Nucleotides frequencies:
  - f(A)=  0.24087
  - f(C)=  0.21994
  - f(G)=  0.25814
  - f(T)=  0.28105
. GTR relative rate parameters :
  A <-> C    1.12670
  A <-> G    2.93015
  A <-> T    0.50957
  C <-> G    0.73224
  C <-> T    2.03103
  G <-> T    1.00000
. Instantaneous rate matrix : 
  [A---------C---------G---------T------]
  -1.11173   0.24010   0.73287   0.13876  
   0.26295  -0.99917   0.18314   0.55307  
   0.68384   0.15604  -1.11219   0.27231  
   0.11892   0.43281   0.25011  -0.80185  


. Run ID:				none
. Random seed:				1692121101
. Subtree patterns aliasing:		no
. Version:				3.3.20211231
. Time used:				0h0m31s (31 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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