Mercurial > repos > iuc > phyml

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children 2bf47d57ebb5
line wrap: on
line source


 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
                                  ---  PhyML 3.3.20190321  ---                                             
                              http://www.atgc-montpellier.fr/phyml                                          
                             Copyright CNRS - Universite Montpellier                                 
 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

. 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.
 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo