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annotate test-data/phylip_phyml_stats.txt @ 3:7c44ad3ab06c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:57:13 +0000
parents 19becf767d4f
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a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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2 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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19becf767d4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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3 --- PhyML 3.3.20190909 ---
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a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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4 http://www.atgc-montpellier.fr/phyml
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5 Copyright CNRS - Universite Montpellier
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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8 . Sequence filename: phylip
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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9 . Data set: #1
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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10 . Initial tree: BioNJ
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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11 . Model of nucleotides substitution: HKY85
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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12 . Number of taxa: 7
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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13 . Log-likelihood: -3113.71269
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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14 . Unconstrained log-likelihood: -3015.37711
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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15 . Composite log-likelihood: -14534.82403
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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16 . Parsimony: 177
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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17 . Tree size: 0.12462
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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18 . Discrete gamma model: Yes
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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19 - Number of classes: 4
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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20 - Gamma shape parameter: 0.774
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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21 - Relative rate in class 1: 0.08994 [freq=0.250000]
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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22 - Relative rate in class 2: 0.39631 [freq=0.250000]
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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23 - Relative rate in class 3: 0.94938 [freq=0.250000]
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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24 - Relative rate in class 4: 2.56437 [freq=0.250000]
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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25 . Transition/transversion ratio: 2.937995
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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26 . Nucleotides frequencies:
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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27 - f(A)= 0.28368
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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28 - f(C)= 0.21846
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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29 - f(G)= 0.26233
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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30 - f(T)= 0.23552
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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31
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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32 . Run ID: none
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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33 . Random seed: 1458308600
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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34 . Subtree patterns aliasing: no
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19becf767d4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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35 . Version: 3.3.20190909
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a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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36 . Time used: 0h0m0s (0 seconds)
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a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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38 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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39 Suggested citations:
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40 S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
a9ee99c3be94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
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41 "New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
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42 Systematic Biology. 2010. 59(3):307-321.
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43
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44 S. Guindon & O. Gascuel
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45 "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
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46 Systematic Biology. 2003. 52(5):696-704.
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47 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo