Mercurial > repos > iuc > phyml

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

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 fd76965826549db42ae414b80e4254089babe6a5
author iuc
date Mon, 23 Oct 2023 17:15:37 +0000
parents 2bf47d57ebb5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
1
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
2 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
3
7157a5b34a68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
iuc
parents: 2
diff changeset
3 --- PhyML 3.3.20220408 ---
0
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
4 http://www.atgc-montpellier.fr/phyml
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
5 Copyright CNRS - Universite Montpellier
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
6 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
7
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
8 . Sequence filename: phylip
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
9 . Data set: #1
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
10 . Initial tree: BioNJ
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
11 . Model of nucleotides substitution: HKY85
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
12 . Number of taxa: 7
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
13 . Log-likelihood: -3113.71269
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
14 . Unconstrained log-likelihood: -3015.37711
3
7157a5b34a68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
iuc
parents: 2
diff changeset
15 . Composite log-likelihood: -14534.82407
0
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
16 . Parsimony: 177
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
17 . Tree size: 0.12462
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
18 . Discrete gamma model: Yes
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
19 - Number of classes: 4
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
20 - Gamma shape parameter: 0.774
3
7157a5b34a68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
iuc
parents: 2
diff changeset
21 - Relative rate in class 1: 0.08995 [freq=0.250000]
7157a5b34a68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
iuc
parents: 2
diff changeset
22 - Relative rate in class 2: 0.39633 [freq=0.250000]
7157a5b34a68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
iuc
parents: 2
diff changeset
23 - Relative rate in class 3: 0.94939 [freq=0.250000]
7157a5b34a68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
iuc
parents: 2
diff changeset
24 - Relative rate in class 4: 2.56433 [freq=0.250000]
7157a5b34a68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
iuc
parents: 2
diff changeset
25 . Transition/transversion ratio: 2.937853
0
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
26 . Nucleotides frequencies:
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
27 - f(A)= 0.28368
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
28 - f(C)= 0.21846
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
29 - f(G)= 0.26233
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
30 - f(T)= 0.23552
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
31
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
32 . Run ID: none
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
33 . Random seed: 1458308600
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
34 . Subtree patterns aliasing: no
3
7157a5b34a68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
iuc
parents: 2
diff changeset
35 . Version: 3.3.20220408
0
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
36 . Time used: 0h0m0s (0 seconds)
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
37
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
38 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
39 Suggested citations:
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
40 S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
41 "New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
42 Systematic Biology. 2010. 59(3):307-321.
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
43
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
44 S. Guindon & O. Gascuel
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
45 "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
46 Systematic Biology. 2003. 52(5):696-704.
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
47 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo