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comparison 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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3 --- PhyML 3.3.20190321 ---
4 http://www.atgc-montpellier.fr/phyml
5 Copyright CNRS - Universite Montpellier
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7
8 . Sequence filename: phylip
9 . Data set: #1
10 . Tree topology search: SPRs
11 . Initial tree: BioNJ
12 . Model of nucleotides substitution: HKY85
13 . Number of taxa: 7
14 . Log-likelihood: -3113.71269
15 . Unconstrained log-likelihood: -3015.37711
16 . Composite log-likelihood: -14534.82403
17 . Parsimony: 177
18 . Tree size: 0.12462
19 . Discrete gamma model: Yes
20 - Number of classes: 4
21 - Gamma shape parameter: 0.774
22 - Relative rate in class 1: 0.08994 [freq=0.250000]
23 - Relative rate in class 2: 0.39631 [freq=0.250000]
24 - Relative rate in class 3: 0.94938 [freq=0.250000]
25 - Relative rate in class 4: 2.56437 [freq=0.250000]
26 . Transition/transversion ratio: 2.937995
27 . Nucleotides frequencies:
28 - f(A)= 0.28368
29 - f(C)= 0.21846
30 - f(G)= 0.26233
31 - f(T)= 0.23552
32
33 . Run ID: none
34 . Random seed: 1458308600
35 . Subtree patterns aliasing: no
36 . Version: 3.3.20190321
37 . Time used: 0h0m0s (0 seconds)
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40 Suggested citations:
41 S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
42 "New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
43 Systematic Biology. 2010. 59(3):307-321.
44
45 S. Guindon & O. Gascuel
46 "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
47 Systematic Biology. 2003. 52(5):696-704.
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