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                                  ---  PhyML 20100914  ---                                             
                            http://www.atgc-montpellier.fr/phyml                                          
                         Copyright CNRS - Universite Montpellier II                                 
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. Sequence filename: 			PF00412.nt.phy
. Data set: 				#1
. Tree topology: 			fixed
. Initial tree: 			user tree (PF00412.nt.phy_starting_tree.txt)
. Model of nucleotides substitution: 	GTR
. Number of taxa: 			40
. Log-likelihood: 			-7698.63982
. Unconstrained likelihood: 		-934.53822
. Parsimony: 				2423
. Tree size: 				23.90041
. Discrete gamma model: 		Yes
  - Number of categories: 		4
  - Gamma shape parameter: 		2.967
. Proportion of invariant: 		0.060
. Nucleotides frequencies:
  - f(A)= 0.27475
  - f(C)= 0.23258
  - f(G)= 0.21571
  - f(T)= 0.27697
. GTR relative rate parameters : 
  A <-> C    2.91160
  A <-> G    4.70922
  A <-> T    1.63859
  C <-> G    4.99646
  C <-> T    5.28705
  G <-> T    1.00000

. Instantaneous rate matrix : 
  [A---------C---------G---------T------]
  -0.86508   0.27287   0.40933   0.18288  
   0.32235  -1.34672   0.43430   0.59007  
   0.52137   0.46826  -1.10124   0.11161  
   0.18141   0.49550   0.08692  -0.76383  



. Run ID:				none
. Random seed:				10
. Subtree patterns aliasing:		no
. Version:				20100914
. Time used:				0h0m19s (19 seconds)

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 Suggested citation:
 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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