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diff test-data/phylip_phyml_stats.txt @ 0:850e213bee26 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
author iuc
date Tue, 28 May 2019 13:53:56 -0400
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children 2bf47d57ebb5
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+++ b/test-data/phylip_phyml_stats.txt	Tue May 28 13:53:56 2019 -0400
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+                                  ---  PhyML 3.3.20190321  ---                                             
+                              http://www.atgc-montpellier.fr/phyml                                          
+                             Copyright CNRS - Universite Montpellier                                 
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+
+. Sequence filename: 			phylip
+. Data set: 				#1
+. Tree topology search: 		SPRs
+. Initial tree: 			BioNJ
+. Model of nucleotides substitution: 	HKY85
+. Number of taxa: 			7
+. Log-likelihood: 			-3113.71269
+. Unconstrained log-likelihood: 	-3015.37711
+. Composite log-likelihood: 		-14534.82403
+. Parsimony: 				177
+. Tree size: 				0.12462
+. Discrete gamma model: 		Yes
+  - Number of classes: 			4
+  - Gamma shape parameter: 		0.774
+  - Relative rate in class 1: 		0.08994 [freq=0.250000] 		
+  - Relative rate in class 2: 		0.39631 [freq=0.250000] 		
+  - Relative rate in class 3: 		0.94938 [freq=0.250000] 		
+  - Relative rate in class 4: 		2.56437 [freq=0.250000] 		
+. Transition/transversion ratio: 	2.937995
+. Nucleotides frequencies:
+  - f(A)=  0.28368
+  - f(C)=  0.21846
+  - f(G)=  0.26233
+  - f(T)=  0.23552
+
+. Run ID:				none
+. Random seed:				1458308600
+. Subtree patterns aliasing:		no
+. Version:				3.3.20190321
+. Time used:				0h0m0s (0 seconds)
+
+ oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
+ 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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