Mercurial > repos > stephenshank > hyphy_gard

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
author stephenshank
date Tue, 30 Oct 2018 10:56:18 -0400
parents 81b2d9fd1284
children
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81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
stephenshank
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0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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2 Loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
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81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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3 Loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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4 Loaded 'IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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5 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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6 Loaded 'convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
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0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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7 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
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81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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8 Already loaded 'libv3/IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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9 Loaded 'libv3/tasks/estimators.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/estimators.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
stephenshank
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10 Loaded '../models/model_functions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/model_functions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
stephenshank
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11 Loaded 'DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
stephenshank
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12 Loaded 'frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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13 Already loaded '../all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
stephenshank
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14 Loaded 'parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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15 Loaded 'GrabBag' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/Utility/GrabBag.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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16 Overwritten previously defined function:'_sortStringsAux'
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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17 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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18 Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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19 Already loaded 'model_functions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/model_functions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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20 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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21 Already loaded 'parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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22 Already loaded 'frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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23 Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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24 Already loaded '../convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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25 Loaded '../models/DNA/GTR.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA/GTR.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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26 Already loaded '../DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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27 Already loaded '../parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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28 Already loaded '../frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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29 Already loaded '../../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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30 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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31 Already loaded '../convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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32 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
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0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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33 Loaded 'libv3/tasks/alignments.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/alignments.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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34 Already loaded '../IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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35 Already loaded '../all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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36 Loaded 'libv3/models/codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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37 Loaded '../tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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38 Loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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39 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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40 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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41 Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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42 Loaded 'libv3/tasks/trees.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/trees.bf
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43 Already loaded '../IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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44 Already loaded '../all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
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45 Already loaded '../convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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46 Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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47 Loaded 'TreeTools' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/TreeTools.ibf
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48 Already loaded 'libv3/tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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49 Loaded 'modules/io_functions.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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50 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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51 Already loaded 'libv3/IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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52 Already loaded 'libv3/convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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53 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
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54 Loaded 'modules/selection_lib.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
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55 Loaded 'libv3/models/codon/BS_REL.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
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56 Already loaded '../codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
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57 Already loaded '../DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
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58 Already loaded '../parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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59 Already loaded '../frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
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60 Already loaded '../../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
81b2d9fd1284 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6438e952ee0a778ceae15f294bd80eb5460455f-dirty
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61 Loaded 'MG_REV.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
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62 Already loaded '../codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
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63 Already loaded '../DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
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64 Already loaded '../parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
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65 Already loaded '../frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
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66 Already loaded '../../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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67 Loaded '../../convenience/math.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/math.bf
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68 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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69 Already loaded 'libv3/convenience/math.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/math.bf
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70 Variable 'NORMALIZE_SEQUENCE_NAMES' was not initialized prior to being used
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71 Loaded 'modules/shared-load-file.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
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72 Variable 'MARKDOWN_OUTPUT' was not initialized prior to being used
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73 Already loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
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74 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
1
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75 Variable 'OWzuGPhH.skipCodeSelectionStep' was not initialized prior to being used
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76 Row and/or column partition is empty. All the data will be used by default.
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77 Variable 'NEXUS_FILE_TREE_MATRIX' was not initialized prior to being used
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78 Variable 'utility.ToggleEnvVariable.cache' was not initialized prior to being used
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79 Variable 'TREE_NODE_NAME_MAPPING' was not initialized prior to being used
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80 Variable 'Gibbjnoz.PROMPT_FOR_FILE' was not initialized prior to being used
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81 Variable 'END_OF_FILE' was not initialized prior to being used
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82 Variable '_DO_TREE_REBALANCE_' was not initialized prior to being used
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83 Variable '_KEEP_I_LABELS_' was not initialized prior to being used
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84 Variable 'INCLUDE_MODEL_SPECS' was not initialized prior to being used
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85 Variable 'utility.ForEachPair.warn_non_rentrant' was not initialized prior to being used
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86 Row and/or column partition is empty. All the data will be used by default.
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87 Row and/or column partition is empty. All the data will be used by default.
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88 Variable 'zpqXEbDu.cache' was not initialized prior to being used
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89 Row and/or column partition is empty. All the data will be used by default.
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90 Variable 'COUNT_GAPS_IN_FREQUENCIES' was not initialized prior to being used
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91 Variable 'NRSKiVtk.model_pi' was not initialized prior to being used
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92 Model NRSKiVtk.model assigned to Pig
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93 Model NRSKiVtk.model assigned to Cow
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94 Model NRSKiVtk.model assigned to Node3
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95 Model NRSKiVtk.model assigned to Horse
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96 Model NRSKiVtk.model assigned to Cat
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97 Model NRSKiVtk.model assigned to Node2
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98 Model NRSKiVtk.model assigned to RhMonkey
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99 Model NRSKiVtk.model assigned to Baboon
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100 Model NRSKiVtk.model assigned to Node9
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101 Model NRSKiVtk.model assigned to Human
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102 Model NRSKiVtk.model assigned to Chimp
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103 Model NRSKiVtk.model assigned to Node12
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104 Model NRSKiVtk.model assigned to Node8
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105 Model NRSKiVtk.model assigned to Node1
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106 Model NRSKiVtk.model assigned to Rat
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107 Model NRSKiVtk.model assigned to Mouse
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108 The tips of the tree:NRSKiVtk.tree_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
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109
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110 Pseudo-optimal path's cost 2330 vs 4284 for 1..k=> a 1.83863 x improvement
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111 Partition 0 reversible model flag computed as 1
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112 Variable 'USE_LAST_RESULTS' was not initialized prior to being used
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113 Variable 'NRSKiVtk.tree_0.Pig.t' was not initialized prior to being used
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114 models.generic.SetBranchLength: NRSKiVtk.tree_0.Pig.t=0.3974535884114245
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115 Variable 'NRSKiVtk.tree_0.Cow.t' was not initialized prior to being used
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116 models.generic.SetBranchLength: NRSKiVtk.tree_0.Cow.t=0.5732857515739808
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117 Variable 'NRSKiVtk.tree_0.Node3.t' was not initialized prior to being used
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118 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node3.t=0.2285810062933711
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119 Variable 'NRSKiVtk.tree_0.Horse.t' was not initialized prior to being used
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120 models.generic.SetBranchLength: NRSKiVtk.tree_0.Horse.t=0.445313802634098
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121 Variable 'NRSKiVtk.tree_0.Cat.t' was not initialized prior to being used
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122 models.generic.SetBranchLength: NRSKiVtk.tree_0.Cat.t=0.7112847618952328
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123 Variable 'NRSKiVtk.tree_0.Node2.t' was not initialized prior to being used
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124 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node2.t=0.1574326532610344
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125 Variable 'NRSKiVtk.tree_0.RhMonkey.t' was not initialized prior to being used
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126 models.generic.SetBranchLength: NRSKiVtk.tree_0.RhMonkey.t=0.00541241057687097
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127 Variable 'NRSKiVtk.tree_0.Baboon.t' was not initialized prior to being used
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128 models.generic.SetBranchLength: NRSKiVtk.tree_0.Baboon.t=0.008348273981595522
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129 Variable 'NRSKiVtk.tree_0.Node9.t' was not initialized prior to being used
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130 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node9.t=0.06106219833449517
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131 Variable 'NRSKiVtk.tree_0.Human.t' was not initialized prior to being used
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132 models.generic.SetBranchLength: NRSKiVtk.tree_0.Human.t=0.01168167424258652
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133 Variable 'NRSKiVtk.tree_0.Chimp.t' was not initialized prior to being used
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134 models.generic.SetBranchLength: NRSKiVtk.tree_0.Chimp.t=0.00214616181187092
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135 Variable 'NRSKiVtk.tree_0.Node12.t' was not initialized prior to being used
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136 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node12.t=0.03189158847602433
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137 Variable 'NRSKiVtk.tree_0.Node8.t' was not initialized prior to being used
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138 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node8.t=0.2735913110261884
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139 Variable 'NRSKiVtk.tree_0.Node1.t' was not initialized prior to being used
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140 models.generic.SetBranchLength: NRSKiVtk.tree_0.Node1.t=0.9154145654683773
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141 Variable 'NRSKiVtk.tree_0.Rat.t' was not initialized prior to being used
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142 models.generic.SetBranchLength: NRSKiVtk.tree_0.Rat.t=0.1368762373082833
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143 Variable 'NRSKiVtk.tree_0.Mouse.t' was not initialized prior to being used
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144 models.generic.SetBranchLength: NRSKiVtk.tree_0.Mouse.t=0.2630995612925615
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145 Variable 'NRSKiVtk.NRSKiVtk.likelihoodFunction' was not initialized prior to being used
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146 Variable 'SAVE_OPT_STATUS_TO' was not initialized prior to being used
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147 Set GUI update interval to every 357-th LF evaluation.
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148 Optimization settings:
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149 OPTIMIZATION_METHOD = 4
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150 OPTIMIZATION_PRECISION = 0.001
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151 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
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152
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153 Initial parameter values
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154
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155 NRSKiVtk.model.theta_GT = 0.25
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156 NRSKiVtk.model.theta_CG = 0.25
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157 NRSKiVtk.model.theta_CT = 1
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158 NRSKiVtk.model.theta_AT = 0.25
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159 NRSKiVtk.model.theta_AC = 0.25
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160 NRSKiVtk.tree_0.Pig.t = 0.397454
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161 NRSKiVtk.tree_0.Cow.t = 0.573286
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162 NRSKiVtk.tree_0.Node3.t = 0.228581
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163 NRSKiVtk.tree_0.Horse.t = 0.445314
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164 NRSKiVtk.tree_0.Cat.t = 0.711285
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165 NRSKiVtk.tree_0.Node2.t = 0.157433
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166 NRSKiVtk.tree_0.RhMonkey.t = 0.00541241
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167 NRSKiVtk.tree_0.Baboon.t = 0.00834827
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168 NRSKiVtk.tree_0.Node9.t = 0.0610622
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169 NRSKiVtk.tree_0.Human.t = 0.0116817
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170 NRSKiVtk.tree_0.Chimp.t = 0.00214616
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171 NRSKiVtk.tree_0.Node12.t = 0.0318916
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172 NRSKiVtk.tree_0.Node8.t = 0.273591
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173 NRSKiVtk.tree_0.Node1.t = 0.915415
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174 NRSKiVtk.tree_0.Rat.t = 0.136876
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175 NRSKiVtk.tree_0.Mouse.t = 0.2631
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176 Optimization finished in 25 loop passes.
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177 1667 likelihood evaluation calls and 12169 matrix exponentiations calls were made
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178
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179 Variable 'BRANCH_LENGTH_STENCIL' was not initialized prior to being used
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180 Variable 'NRSKiVtk.option' was not initialized prior to being used
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181 Variable 'busted.terms.json.nucleotide_gtr' was not initialized prior to being used
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182 Variable 'Unknown' was not initialized prior to being used
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183 Variable 'ThTEDPSn.initial_value' was not initialized prior to being used
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184 Variable 'dIONygHy.data_filter' was not initialized prior to being used
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185 Row and/or column partition is empty. All the data will be used by default.
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186 Set GUI update interval to every 2834-th LF evaluation.
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187 Optimization settings:
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188 OPTIMIZATION_METHOD = 4
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189 OPTIMIZATION_PRECISION = 0.001
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190 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
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191
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192 Initial parameter values
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193
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194 frequencies._aux.CF3x4.p0_0 = 0.415775
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195 frequencies._aux.CF3x4.p0_1 = 0.250343
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196 frequencies._aux.CF3x4.p0_2 = 0.652625
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197 frequencies._aux.CF3x4.p1_0 = 0.399465
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198 frequencies._aux.CF3x4.p1_1 = 0.28317
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199 frequencies._aux.CF3x4.p1_2 = 0.391304
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200 frequencies._aux.CF3x4.p2_0 = 0.253743
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201 frequencies._aux.CF3x4.p2_1 = 0.314941
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202 frequencies._aux.CF3x4.p2_2 = 0.521444
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203 Optimization finished in 5 loop passes.
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204 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
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205
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206 Variable 'dIONygHy.model_MGREV_pi' was not initialized prior to being used
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207 Model dIONygHy.model_MGREV assigned to Pig
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208 Model dIONygHy.model_MGREV assigned to Cow
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209 Model dIONygHy.model_MGREV assigned to Node3
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210 Model dIONygHy.model_MGREV assigned to Horse
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211 Model dIONygHy.model_MGREV assigned to Cat
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212 Model dIONygHy.model_MGREV assigned to Node2
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213 Model dIONygHy.model_MGREV assigned to RhMonkey
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214 Model dIONygHy.model_MGREV assigned to Baboon
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215 Model dIONygHy.model_MGREV assigned to Node9
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216 Model dIONygHy.model_MGREV assigned to Human
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217 Model dIONygHy.model_MGREV assigned to Chimp
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218 Model dIONygHy.model_MGREV assigned to Node12
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219 Model dIONygHy.model_MGREV assigned to Node8
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220 Model dIONygHy.model_MGREV assigned to Node1
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221 Model dIONygHy.model_MGREV assigned to Rat
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222 Model dIONygHy.model_MGREV assigned to Mouse
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223 The tips of the tree:dIONygHy.tree_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
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224
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225 Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
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226 Partition 0 reversible model flag computed as 1
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227 Variable 'dIONygHy.dIONygHy.likelihoodFunction' was not initialized prior to being used
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228 Variable 'dIONygHy.tree_0.Pig.alpha' was not initialized prior to being used
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229 Variable 'dIONygHy.tree_0.Cow.alpha' was not initialized prior to being used
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230 Variable 'dIONygHy.tree_0.Node3.alpha' was not initialized prior to being used
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231 Variable 'dIONygHy.tree_0.Horse.alpha' was not initialized prior to being used
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232 Variable 'dIONygHy.tree_0.Cat.alpha' was not initialized prior to being used
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233 Variable 'dIONygHy.tree_0.Node2.alpha' was not initialized prior to being used
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234 Variable 'dIONygHy.tree_0.RhMonkey.alpha' was not initialized prior to being used
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235 Variable 'dIONygHy.tree_0.Baboon.alpha' was not initialized prior to being used
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236 Variable 'dIONygHy.tree_0.Node9.alpha' was not initialized prior to being used
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237 Variable 'dIONygHy.tree_0.Human.alpha' was not initialized prior to being used
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238 Variable 'dIONygHy.tree_0.Chimp.alpha' was not initialized prior to being used
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239 Variable 'dIONygHy.tree_0.Node12.alpha' was not initialized prior to being used
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240 Variable 'dIONygHy.tree_0.Node8.alpha' was not initialized prior to being used
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241 Variable 'dIONygHy.tree_0.Node1.alpha' was not initialized prior to being used
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242 Variable 'dIONygHy.tree_0.Rat.alpha' was not initialized prior to being used
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243 Variable 'dIONygHy.tree_0.Mouse.alpha' was not initialized prior to being used
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244 Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
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245 Set GUI update interval to every 208-th LF evaluation.
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246 Initial guess for dIONygHy.tree_0.Node2.alpha is 0.000173618
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247 Initial guess for dIONygHy.tree_0.Node3.alpha is 1.15458e-05
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248 Initial guess for dIONygHy.tree_0.Pig.alpha is 0.000173063
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249 Initial guess for dIONygHy.tree_0.Cow.alpha is 0.000186779
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250 Initial guess for dIONygHy.tree_0.Horse.alpha is 0.000174488
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251 Initial guess for dIONygHy.tree_0.Cat.alpha is 0.000196799
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252 Initial guess for dIONygHy.tree_0.Node8.alpha is 4.67029e-05
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253 Initial guess for dIONygHy.tree_0.Node9.alpha is 0.000140119
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254 Initial guess for dIONygHy.tree_0.RhMonkey.alpha is 4.64183e-06
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255 Initial guess for dIONygHy.tree_0.Baboon.alpha is 1.75863e-06
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256 Initial guess for dIONygHy.tree_0.Node12.alpha is 2.75759e-05
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257 Initial guess for dIONygHy.tree_0.Human.alpha is 7.93383e-07
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258 Initial guess for dIONygHy.tree_0.Chimp.alpha is 1.32491e-06
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259 Initial guess for dIONygHy.tree_0.Rat.alpha is 8.26646e-05
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260 Initial guess for dIONygHy.tree_0.Mouse.alpha is 0.000107933
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261 Optimization settings:
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262 OPTIMIZATION_METHOD = 4
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263 OPTIMIZATION_PRECISION = 0.001
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264 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
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265
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266 Initial parameter values
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267
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268 dIONygHy.model_MGREV.theta_CT = 1
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269 dIONygHy.model_MGREV.theta_GT = 1
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270 dIONygHy.model_MGREV.theta_CG = 1
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271 dIONygHy.model_MGREV.theta_AC = 1
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272 dIONygHy.model_MGREV.theta_AT = 1
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273 dIONygHy.model_MGREV.omega_0 = 1
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274 dIONygHy.tree_0.Pig.alpha = 0.000173063
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275 dIONygHy.tree_0.Cow.alpha = 0.000186779
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276 dIONygHy.tree_0.Node3.alpha = 1.15458e-05
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277 dIONygHy.tree_0.Horse.alpha = 0.000174488
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278 dIONygHy.tree_0.Cat.alpha = 0.000196799
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279 dIONygHy.tree_0.Node2.alpha = 0.000173618
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280 dIONygHy.tree_0.RhMonkey.alpha = 4.64183e-06
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281 dIONygHy.tree_0.Baboon.alpha = 1.75863e-06
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282 dIONygHy.tree_0.Node9.alpha = 0.000140119
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283 dIONygHy.tree_0.Human.alpha = 7.93383e-07
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284 dIONygHy.tree_0.Chimp.alpha = 1.32491e-06
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285 dIONygHy.tree_0.Node12.alpha = 2.75759e-05
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286 dIONygHy.tree_0.Node8.alpha = 4.67029e-05
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287 dIONygHy.tree_0.Node1.alpha = 0.1
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288 dIONygHy.tree_0.Rat.alpha = 8.26646e-05
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289 dIONygHy.tree_0.Mouse.alpha = 0.000107933
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290 Optimization finished in 35 loop passes.
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291 3927 likelihood evaluation calls and 23083 matrix exponentiations calls were made
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292
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293 Row and/or column partition is empty. All the data will be used by default.
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294 Set GUI update interval to every 2909-th LF evaluation.
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295 Optimization settings:
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296 OPTIMIZATION_METHOD = 4
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297 OPTIMIZATION_PRECISION = 0.001
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298 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
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299
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300 Initial parameter values
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301
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302 frequencies._aux.CF3x4.p0_0 = 0.415775
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303 frequencies._aux.CF3x4.p0_1 = 0.250343
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304 frequencies._aux.CF3x4.p0_2 = 0.652625
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305 frequencies._aux.CF3x4.p1_0 = 0.399465
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306 frequencies._aux.CF3x4.p1_1 = 0.28317
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307 frequencies._aux.CF3x4.p1_2 = 0.391304
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308 frequencies._aux.CF3x4.p2_0 = 0.253743
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309 frequencies._aux.CF3x4.p2_1 = 0.314941
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310 frequencies._aux.CF3x4.p2_2 = 0.521444
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311 Optimization finished in 5 loop passes.
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312 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
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313
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314 Variable 'dIONygHy.model_MGREV_pi' was not initialized prior to being used
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315 Model dIONygHy.model_MGREV assigned to Pig
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316 Model dIONygHy.model_MGREV assigned to Cow
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317 Model dIONygHy.model_MGREV assigned to Node3
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318 Model dIONygHy.model_MGREV assigned to Horse
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319 Model dIONygHy.model_MGREV assigned to Cat
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320 Model dIONygHy.model_MGREV assigned to Node2
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321 Model dIONygHy.model_MGREV assigned to RhMonkey
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322 Model dIONygHy.model_MGREV assigned to Baboon
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323 Model dIONygHy.model_MGREV assigned to Node9
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324 Model dIONygHy.model_MGREV assigned to Human
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325 Model dIONygHy.model_MGREV assigned to Chimp
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326 Model dIONygHy.model_MGREV assigned to Node12
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327 Model dIONygHy.model_MGREV assigned to Node8
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328 Model dIONygHy.model_MGREV assigned to Node1
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329 Model dIONygHy.model_MGREV assigned to Rat
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330 Model dIONygHy.model_MGREV assigned to Mouse
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331 The tips of the tree:dIONygHy.tree_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
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332
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333 Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
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334 Partition 0 reversible model flag computed as 1
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335 Variable 'dIONygHy.tree_0.Node1.alpha' was not initialized prior to being used
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336 Variable 'dIONygHy.tree_0.Node8.alpha' was not initialized prior to being used
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337 Variable 'dIONygHy.tree_0.Rat.alpha' was not initialized prior to being used
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338 Variable 'dIONygHy.tree_0.Node12.alpha' was not initialized prior to being used
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339 Variable 'dIONygHy.tree_0.Cat.alpha' was not initialized prior to being used
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340 Variable 'dIONygHy.tree_0.Chimp.alpha' was not initialized prior to being used
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341 Variable 'dIONygHy.tree_0.Human.alpha' was not initialized prior to being used
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342 Variable 'dIONygHy.tree_0.Node9.alpha' was not initialized prior to being used
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343 Variable 'dIONygHy.tree_0.Baboon.alpha' was not initialized prior to being used
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344 Variable 'dIONygHy.tree_0.Node2.alpha' was not initialized prior to being used
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345 Variable 'dIONygHy.tree_0.RhMonkey.alpha' was not initialized prior to being used
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346 Variable 'dIONygHy.tree_0.Node3.alpha' was not initialized prior to being used
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347 Variable 'dIONygHy.tree_0.Cow.alpha' was not initialized prior to being used
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348 Variable 'dIONygHy.tree_0.Pig.alpha' was not initialized prior to being used
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349 Variable 'dIONygHy.tree_0.Horse.alpha' was not initialized prior to being used
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350 Variable 'dIONygHy.tree_0.Mouse.alpha' was not initialized prior to being used
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351 Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
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352 Set GUI update interval to every 269-th LF evaluation.
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353 Initial guess for dIONygHy.tree_0.Node2.alpha is 0.000173618
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354 Initial guess for dIONygHy.tree_0.Node3.alpha is 1.15458e-05
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355 Initial guess for dIONygHy.tree_0.Pig.alpha is 0.000173063
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356 Initial guess for dIONygHy.tree_0.Cow.alpha is 0.000186779
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357 Initial guess for dIONygHy.tree_0.Horse.alpha is 0.000174488
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358 Initial guess for dIONygHy.tree_0.Cat.alpha is 0.000196799
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359 Initial guess for dIONygHy.tree_0.Node8.alpha is 4.67029e-05
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360 Initial guess for dIONygHy.tree_0.Node9.alpha is 0.000140119
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361 Initial guess for dIONygHy.tree_0.RhMonkey.alpha is 4.64183e-06
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362 Initial guess for dIONygHy.tree_0.Baboon.alpha is 1.75863e-06
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363 Initial guess for dIONygHy.tree_0.Node12.alpha is 2.75759e-05
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364 Initial guess for dIONygHy.tree_0.Human.alpha is 7.93383e-07
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365 Initial guess for dIONygHy.tree_0.Chimp.alpha is 1.32491e-06
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366 Initial guess for dIONygHy.tree_0.Rat.alpha is 8.26646e-05
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367 Initial guess for dIONygHy.tree_0.Mouse.alpha is 0.000107933
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368 Optimization settings:
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369 OPTIMIZATION_METHOD = 4
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370 OPTIMIZATION_PRECISION = 0.001
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371 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
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372
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373 Initial parameter values
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374
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375 dIONygHy.model_MGREV.theta_CG = 1
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376 dIONygHy.model_MGREV.theta_AT = 1
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377 dIONygHy.model_MGREV.theta_CT = 1
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
378 dIONygHy.model_MGREV.theta_GT = 1
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
379 dIONygHy.model_MGREV.theta_AC = 1
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
380 dIONygHy.model_MGREV.omega_0 = 1
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
381 dIONygHy.tree_0.Pig.alpha = 0.000173063
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
382 dIONygHy.tree_0.Cow.alpha = 0.000186779
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
383 dIONygHy.tree_0.Node3.alpha = 1.15458e-05
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
384 dIONygHy.tree_0.Horse.alpha = 0.000174488
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
385 dIONygHy.tree_0.Cat.alpha = 0.000196799
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
386 dIONygHy.tree_0.Node2.alpha = 0.000173618
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
387 dIONygHy.tree_0.RhMonkey.alpha = 4.64183e-06
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
388 dIONygHy.tree_0.Baboon.alpha = 1.75863e-06
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
389 dIONygHy.tree_0.Node9.alpha = 0.000140119
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
390 dIONygHy.tree_0.Human.alpha = 7.93383e-07
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
391 dIONygHy.tree_0.Chimp.alpha = 1.32491e-06
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
392 dIONygHy.tree_0.Node12.alpha = 2.75759e-05
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
393 dIONygHy.tree_0.Node8.alpha = 4.67029e-05
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
394 dIONygHy.tree_0.Node1.alpha = 0.1
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
395 dIONygHy.tree_0.Rat.alpha = 8.26646e-05
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
396 dIONygHy.tree_0.Mouse.alpha = 0.000107933
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
397 Optimization finished in 35 loop passes.
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
398 3276 likelihood evaluation calls and 21044 matrix exponentiations calls were made
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
399
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
400 Overwritten previously defined function:'IIsiGihg.rate_generator'
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
401 Overwritten previously defined function:'IIsiGihg.rate_generator'
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
402 Set GUI update interval to every 3023-th LF evaluation.
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
403 Optimization settings:
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
404 OPTIMIZATION_METHOD = 4
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
405 OPTIMIZATION_PRECISION = 0.001
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
406 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
407
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
408 Initial parameter values
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
409
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
410 frequencies._aux.CF3x4.p0_0 = 0.415775
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
411 frequencies._aux.CF3x4.p0_1 = 0.250343
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
412 frequencies._aux.CF3x4.p0_2 = 0.652625
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
413 frequencies._aux.CF3x4.p1_0 = 0.399465
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
414 frequencies._aux.CF3x4.p1_1 = 0.28317
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
415 frequencies._aux.CF3x4.p1_2 = 0.391304
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
416 frequencies._aux.CF3x4.p2_0 = 0.253743
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
417 frequencies._aux.CF3x4.p2_1 = 0.314941
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
418 frequencies._aux.CF3x4.p2_2 = 0.521444
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
419 Optimization finished in 5 loop passes.
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
420 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
421
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
422 Variable 'busted.test_pi' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
423 Overwritten previously defined function:'IIsiGihg.rate_generator'
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
424 Overwritten previously defined function:'IIsiGihg.rate_generator'
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
425 Overwritten previously defined function:'IIsiGihg.rate_generator'
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
426 Set GUI update interval to every 3010-th LF evaluation.
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
427 Optimization settings:
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
428 OPTIMIZATION_METHOD = 4
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
429 OPTIMIZATION_PRECISION = 0.001
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
430 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
431
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
432 Initial parameter values
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
433
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
434 frequencies._aux.CF3x4.p0_0 = 0.415775
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
435 frequencies._aux.CF3x4.p0_1 = 0.250343
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
436 frequencies._aux.CF3x4.p0_2 = 0.652625
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
437 frequencies._aux.CF3x4.p1_0 = 0.399465
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
438 frequencies._aux.CF3x4.p1_1 = 0.28317
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
439 frequencies._aux.CF3x4.p1_2 = 0.391304
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
440 frequencies._aux.CF3x4.p2_0 = 0.253743
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
441 frequencies._aux.CF3x4.p2_1 = 0.314941
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
442 frequencies._aux.CF3x4.p2_2 = 0.521444
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
443 Optimization finished in 5 loop passes.
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
444 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
445
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
446 Variable 'busted.background_pi' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
447 Variable 'ASSUME_REVERSIBLE_MODELS' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
448 No nodel was assigned to Pig
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
449 No nodel was assigned to Cow
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
450 No nodel was assigned to Node3
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
451 No nodel was assigned to Horse
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
452 No nodel was assigned to Cat
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
453 No nodel was assigned to Node2
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
454 No nodel was assigned to RhMonkey
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
455 No nodel was assigned to Baboon
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
456 No nodel was assigned to Node9
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
457 No nodel was assigned to Human
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
458 No nodel was assigned to Chimp
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
459 No nodel was assigned to Node12
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
460 No nodel was assigned to Node8
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
461 No nodel was assigned to Node1
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
462 No nodel was assigned to Rat
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
463 No nodel was assigned to Mouse
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
464 The tips of the tree:CPXgZuSs.tree_id_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
465
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
466 Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
467 Partition 0 is ASSUMED to have a reversible model
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
468 busted.test.theta_AG was already constrained in estimators.SetGlobals2
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
469 Variable 'CPXgZuSs.tree_id_0.Pig.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
470 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Pig.t=1.377886710534728
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
471 Variable 'CPXgZuSs.tree_id_0.Cow.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
472 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Cow.t=1.774251775766245
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
473 Variable 'CPXgZuSs.tree_id_0.Node3.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
474 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node3.t=0.727900992785442
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
475 Variable 'CPXgZuSs.tree_id_0.Horse.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
476 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Horse.t=1.51058601207266
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
477 Variable 'CPXgZuSs.tree_id_0.Cat.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
478 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Cat.t=1.957296993203762
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
479 Variable 'CPXgZuSs.tree_id_0.Node2.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
480 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node2.t=0.4612561973173576
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
481 Variable 'CPXgZuSs.tree_id_0.RhMonkey.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
482 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.RhMonkey.t=0.02659579655381833
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
483 Variable 'CPXgZuSs.tree_id_0.Baboon.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
484 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Baboon.t=0.01267390527294645
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
485 Variable 'CPXgZuSs.tree_id_0.Node9.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
486 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node9.t=0.1855677984720407
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
487 Variable 'CPXgZuSs.tree_id_0.Human.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
488 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Human.t=0
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
489 Variable 'CPXgZuSs.tree_id_0.Chimp.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
490 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Chimp.t=0.01307822802283968
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
491 Variable 'CPXgZuSs.tree_id_0.Node12.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
492 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node12.t=0.1279673910082466
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
493 Variable 'CPXgZuSs.tree_id_0.Node8.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
494 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node8.t=0.7824909790907859
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
495 Variable 'CPXgZuSs.tree_id_0.Node1.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
496 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node1.t=2.034207610785829
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
497 Variable 'CPXgZuSs.tree_id_0.Rat.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
498 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Rat.t=0.4799151894651191
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
499 Variable 'CPXgZuSs.tree_id_0.Mouse.t' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
500 models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Mouse.t=0.859781481367942
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
501 Variable 'CPXgZuSs.CPXgZuSs.likelihoodFunction' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
502 Set GUI update interval to every 17-th LF evaluation.
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
503 Optimization settings:
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
504 OPTIMIZATION_METHOD = 4
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
505 OPTIMIZATION_PRECISION = 0.001
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
506 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
507
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
508 Initial parameter values
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
509
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
510 busted.test.theta_AC = 0.575889
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
511 busted.test.theta_AT = 0.266515
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
512 busted.test.omega1 = 0
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
513 busted.test.bsrel_mixture_aux_0 = 0.7
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
514 busted.test.theta_CG = 0.470944
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
515 busted.test.omega3 = 9.52381
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
516 busted.test.omega2 = 0.238095
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
517 busted.test.theta_CT = 0.973284
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
518 busted.test.bsrel_mixture_aux_1 = 0.666667
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
519 busted.test.theta_GT = 0.315964
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
520 CPXgZuSs.tree_id_0.Pig.t = 1.37789
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
521 CPXgZuSs.tree_id_0.Cow.t = 1.77425
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
522 CPXgZuSs.tree_id_0.Node3.t = 0.727901
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
523 CPXgZuSs.tree_id_0.Horse.t = 1.51059
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
524 CPXgZuSs.tree_id_0.Cat.t = 1.9573
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
525 CPXgZuSs.tree_id_0.Node2.t = 0.461256
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
526 CPXgZuSs.tree_id_0.RhMonkey.t = 0.0265958
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
527 CPXgZuSs.tree_id_0.Baboon.t = 0.0126739
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
528 CPXgZuSs.tree_id_0.Node9.t = 0.185568
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
529 CPXgZuSs.tree_id_0.Human.t = 0
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
530 CPXgZuSs.tree_id_0.Chimp.t = 0.0130782
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
531 CPXgZuSs.tree_id_0.Node12.t = 0.127967
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
532 CPXgZuSs.tree_id_0.Node8.t = 0.782491
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
533 CPXgZuSs.tree_id_0.Node1.t = 2.03421
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
534 CPXgZuSs.tree_id_0.Rat.t = 0.479915
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
535 CPXgZuSs.tree_id_0.Mouse.t = 0.859781
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
536 Optimization finished in 26 loop passes.
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
537 2990 likelihood evaluation calls and 70968 matrix exponentiations calls were made
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
538
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
539 Variable 'KIGDLXKi.CPXgZuSs.likelihoodFunction' was not initialized prior to being used
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
540 Set GUI update interval to every 28-th LF evaluation.
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
541 Optimization settings:
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
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diff changeset
542 OPTIMIZATION_METHOD = 4
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
543 OPTIMIZATION_PRECISION = 0.001
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
544 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
545
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
546 Initial parameter values
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
547
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
548 busted.test.theta_AC = 0.468589
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
549 busted.test.omega1 = 0.210733
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
550 busted.test.bsrel_mixture_aux_0 = 0.412135
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
551 busted.test.theta_AT = 0.215633
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
552 busted.test.omega2 = 0.105287
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
553 busted.test.bsrel_mixture_aux_1 = 0.404693
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
554 busted.test.theta_CT = 0.973171
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
555 busted.test.theta_GT = 0.273282
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
556 busted.test.theta_CG = 0.415669
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
557 CPXgZuSs.tree_id_0.Pig.t = 0.410826
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
558 CPXgZuSs.tree_id_0.Cow.t = 0.555921
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
559 CPXgZuSs.tree_id_0.Node3.t = 0.241332
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
560 CPXgZuSs.tree_id_0.Horse.t = 0.483056
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
561 CPXgZuSs.tree_id_0.Cat.t = 0.61829
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
562 CPXgZuSs.tree_id_0.Node2.t = 0.117184
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
563 CPXgZuSs.tree_id_0.RhMonkey.t = 0.00689772
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
564 CPXgZuSs.tree_id_0.Baboon.t = 0.0034792
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
565 CPXgZuSs.tree_id_0.Node9.t = 0.051855
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
566 CPXgZuSs.tree_id_0.Human.t = 0
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
567 CPXgZuSs.tree_id_0.Chimp.t = 0.00344635
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
568 CPXgZuSs.tree_id_0.Node12.t = 0.0343399
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
569 CPXgZuSs.tree_id_0.Node8.t = 0.253166
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
570 CPXgZuSs.tree_id_0.Node1.t = 0.86218
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
571 CPXgZuSs.tree_id_0.Rat.t = 0.138343
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
572 CPXgZuSs.tree_id_0.Mouse.t = 0.279774
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
573 Optimization finished in 14 loop passes.
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
574 1338 likelihood evaluation calls and 35802 matrix exponentiations calls were made
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
575
0ea9da9cd6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
stephenshank
parents: 0
diff changeset
576 Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used