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                                  ---  PhyML 3.3.20220408  ---                                             
                              http://www.atgc-montpellier.fr/phyml                                          
                             Copyright CNRS - Universite Montpellier                                 
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. Sequence filename: 			primates-nt.phy
. Data set: 				#1
. Initial tree: 			user tree (/Users/pece/Repositories/Selection-in-Genes-Course/tutorials/parameter-estimation/data/primates-nt.newick)
. Model of nucleotides substitution: 	HKY85
. Number of taxa: 			20
. Log-likelihood: 			-6173.49644
. Unconstrained log-likelihood: 	-5060.29926
. Composite log-likelihood: 		-41505.63449
. Parsimony: 				739
. Tree size: 				0.54587
. Discrete gamma model: 		Yes
  - Number of classes: 			4
  - Gamma shape parameter: 		0.557
  - Relative rate in class 1: 		0.04447 [freq=0.250000] 		
  - Relative rate in class 2: 		0.28777 [freq=0.250000] 		
  - Relative rate in class 3: 		0.85795 [freq=0.250000] 		
  - Relative rate in class 4: 		2.80982 [freq=0.250000] 		
. Transition/transversion ratio: 	3.258424
. Nucleotides frequencies:
  - f(A)=  0.28546
  - f(C)=  0.21267
  - f(G)=  0.25785
  - f(T)=  0.24401

. Run ID:				empirical
. Random seed:				1651860431
. Subtree patterns aliasing:		no
. Version:				3.3.20220408
. Time used:				0h0m0s (0 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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