Mercurial > repos > iuc > phyml

annotate 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
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
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
3 --- PhyML 3.3.20190321 ---
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 . Tree topology search: SPRs
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
11 . Initial tree: BioNJ
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
12 . 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
13 . 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
14 . 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
15 . Unconstrained log-likelihood: -3015.37711
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
16 . Composite log-likelihood: -14534.82403
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
17 . Parsimony: 177
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
18 . 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
19 . 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
20 - 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
21 - Gamma shape parameter: 0.774
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
22 - Relative rate in class 1: 0.08994 [freq=0.250000]
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
23 - Relative rate in class 2: 0.39631 [freq=0.250000]
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
24 - Relative rate in class 3: 0.94938 [freq=0.250000]
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
25 - Relative rate in class 4: 2.56437 [freq=0.250000]
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
26 . Transition/transversion ratio: 2.937995
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
27 . Nucleotides frequencies:
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
28 - 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
29 - 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
30 - 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
31 - 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
32
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
33 . Run ID: none
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
34 . Random seed: 1458308600
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
35 . Subtree patterns aliasing: no
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
36 . Version: 3.3.20190321
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
37 . 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
38
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
39 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
40 Suggested citations:
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
41 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
42 "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
43 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
44
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
45 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
46 "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
47 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
48 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo