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                                    ---  PhyML v3.0_360-500M  ---
                            http://www.atgc-montpellier.fr/phyml
                         Copyright CNRS - Universite Montpellier II
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. Sequence filename: 			Example_Alignement

. Data set: 				#1

. Tree topology search : 		Best of NNIs and SPRs

. Initial tree: 			BioNJ

. Model of nucleotides substitution: 	GTR

. Number of taxa: 			104

. Log-likelihood: 			-48380.82650

. Unconstrained likelihood: 		-14205.64537

. Parsimony: 				12660

. Tree size: 				37.97749

. Discrete gamma model: 		Yes
  - Number of categories: 		4
  - Gamma shape parameter: 		0.687

. Proportion of invariant: 		0.133

. Nucleotides frequencies:

  - f(A)= 0.25062
  - f(C)= 0.20983
  - f(G)= 0.23165
  - f(T)= 0.30789

. GTR relative rate parameters :

  A <-> C    1.19324
  A <-> G    2.18622
  A <-> T    1.67963
  C <-> G    0.84982
  C <-> T    2.63215
  G <-> T    1.00000


. Instantaneous rate matrix :

  [A---------C---------G---------T------]
  -1.05817   0.20797   0.42066   0.42954
   0.24840  -1.08505   0.16352   0.67314
   0.45510   0.14811  -0.85895   0.25574
   0.34964   0.45875   0.19241  -1.00081



. Time used 0h37m0s


. 2220 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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