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comparison test-data/phylip_phyml_stats.txt @ 3:7157a5b34a68 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
author iuc
date Mon, 23 Oct 2023 17:15:37 +0000
parents 2bf47d57ebb5
children
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2:2bf47d57ebb5 3:7157a5b34a68
1 1
2 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
3 --- PhyML 3.3.20190909 --- 3 --- PhyML 3.3.20220408 ---
4 http://www.atgc-montpellier.fr/phyml 4 http://www.atgc-montpellier.fr/phyml
5 Copyright CNRS - Universite Montpellier 5 Copyright CNRS - Universite Montpellier
6 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 6 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
7 7
8 . Sequence filename: phylip 8 . Sequence filename: phylip
10 . Initial tree: BioNJ 10 . Initial tree: BioNJ
11 . Model of nucleotides substitution: HKY85 11 . Model of nucleotides substitution: HKY85
12 . Number of taxa: 7 12 . Number of taxa: 7
13 . Log-likelihood: -3113.71269 13 . Log-likelihood: -3113.71269
14 . Unconstrained log-likelihood: -3015.37711 14 . Unconstrained log-likelihood: -3015.37711
15 . Composite log-likelihood: -14534.82403 15 . Composite log-likelihood: -14534.82407
16 . Parsimony: 177 16 . Parsimony: 177
17 . Tree size: 0.12462 17 . Tree size: 0.12462
18 . Discrete gamma model: Yes 18 . Discrete gamma model: Yes
19 - Number of classes: 4 19 - Number of classes: 4
20 - Gamma shape parameter: 0.774 20 - Gamma shape parameter: 0.774
21 - Relative rate in class 1: 0.08994 [freq=0.250000] 21 - Relative rate in class 1: 0.08995 [freq=0.250000]
22 - Relative rate in class 2: 0.39631 [freq=0.250000] 22 - Relative rate in class 2: 0.39633 [freq=0.250000]
23 - Relative rate in class 3: 0.94938 [freq=0.250000] 23 - Relative rate in class 3: 0.94939 [freq=0.250000]
24 - Relative rate in class 4: 2.56437 [freq=0.250000] 24 - Relative rate in class 4: 2.56433 [freq=0.250000]
25 . Transition/transversion ratio: 2.937995 25 . Transition/transversion ratio: 2.937853
26 . Nucleotides frequencies: 26 . Nucleotides frequencies:
27 - f(A)= 0.28368 27 - f(A)= 0.28368
28 - f(C)= 0.21846 28 - f(C)= 0.21846
29 - f(G)= 0.26233 29 - f(G)= 0.26233
30 - f(T)= 0.23552 30 - f(T)= 0.23552
31 31
32 . Run ID: none 32 . Run ID: none
33 . Random seed: 1458308600 33 . Random seed: 1458308600
34 . Subtree patterns aliasing: no 34 . Subtree patterns aliasing: no
35 . Version: 3.3.20190909 35 . Version: 3.3.20220408
36 . Time used: 0h0m0s (0 seconds) 36 . Time used: 0h0m0s (0 seconds)
37 37
38 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 38 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
39 Suggested citations: 39 Suggested citations:
40 S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel 40 S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel