Mercurial > repos > rdvelazquez > hyphy_relax
changeset 4:7782bb7bc7b7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
| author | rdvelazquez |
|---|---|
| date | Tue, 12 Feb 2019 08:53:39 -0500 |
| parents | 0648b03f1d2f |
| children | eb2be688941a |
| files | hyphy_relax.xml test-data/hyphy-in1.nhx test-data/messages.log test-data/relax-in1.nhx test-data/relax-in2.nhx test-data/relax-out1.json |
| diffstat | 6 files changed, 897 insertions(+), 144 deletions(-) [+] |
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--- a/hyphy_relax.xml Mon Feb 11 20:18:43 2019 -0500 +++ b/hyphy_relax.xml Tue Feb 12 08:53:39 2019 -0500 @@ -1,20 +1,19 @@ <?xml version="1.0"?> <tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0"> - <description>Detect relaxed selection in a codon-based phylogenetic framework</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="version_command" /> - <command detect_errors="exit_code"> - <![CDATA[ + <description>Detect relaxed selection in a codon-based + phylogenetic framework</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ #if $treeAnnotations == 2: ln -s '$input_file' relax_input.fa && ln -s '$input_nhx' relax_input.nhx && echo $gencodeid > tool_params && echo `pwd`/relax_input.fa >> tool_params && echo `pwd`/relax_input.nhx >> tool_params && - echo '$treeAnnotations' >> tool_params && echo '3' && echo '2' && echo '$analysisType' >> tool_params && @@ -25,42 +24,38 @@ echo $gencodeid > tool_params && echo `pwd`/relax_input.fa >> tool_params && echo `pwd`/relax_input.nhx >> tool_params && - echo '$treeAnnotations' >> tool_params && echo '2' && echo '$analysisType' >> tool_params && @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' #end if - ]]> - </command> - <inputs> - <expand macro="inputs" /> - <expand macro="gencode" /> - <param name="analysisType" type="select" label="Analysis Type"> - <option value="1">All</option> - <option value="2">Minimal</option> - </param> - <param name="treeAnnotations" type="select" label="Tree Annotations"> - <option value="1">TEST only</option> - <option value="2">TEST and REFERENCE</option> - </param> - </inputs> - <outputs> - <data name="relax_log" format="txt" /> - <data name="relax_output" format="hyphy_json_results" from_work_dir="relax_input.fa.RELAX.json" /> - </outputs> - <tests> - <test> - <param name="input_file" ftype="fasta" value="relax-in1.fa" /> - <param name="input_nhx" ftype="nhx" value="relax-in1.nhx" /> - <output name="relax_output" file="relax-out1.json" compare="sim_size" /> - </test> - </tests> - <help> - <![CDATA[ + ]]></command> + <inputs> + <expand macro="inputs"/> + <expand macro="gencode"/> + <param name="analysisType" type="select" label="Analysis Type"> + <option value="1">All</option> + <option value="2">Minimal</option> + </param> + <param name="treeAnnotations" type="select" label="Tree Annotations"> + <option value="1">TEST only</option> + <option value="2">TEST and REFERENCE</option> + </param> + </inputs> + <outputs> + <data name="relax_log" format="txt"/> + <data name="relax_output" format="hyphy_json_results" from_work_dir="relax_input.fa.RELAX.json"/> + </outputs> + <tests> + <test> + <param name="input_file" ftype="fasta" value="relax-in1.fa"/> + <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/> + <output name="relax_output" file="relax-out1.json" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ RELAX (Detect relaxed selection in a codon-based phylogenetic framework) - ]]> - </help> - <expand macro="citations"> - <citation type="doi">10.1093/molbev/msu400</citation> - </expand> + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1093/molbev/msu400</citation> + </expand> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hyphy-in1.nhx Tue Feb 12 08:53:39 2019 -0500 @@ -0,0 +1,1 @@ +((KF790010:0.001247,CY147300:0.000623):0.0,((CY168239:0.001872,(CY171039:0.001874,KF790389:0.000623):0.000624):0.0,((CY141224:0.001247,(CY147305:0.0,KF790037:0.000623):0.000623):0.0,(((KF790403:0.000623,KF761507:0.001876):0.0,KC526205:0.000623):0.0,((CY169303:0.0,(KF789585:0.000623,CY141202:0.000623):0.000623):0.000623,(((KJ667974:0.002501,KJ938675:0.001873):0.000623,CY134876:0.0):0.000623,((KF790414:0.001248,(KF790384:0.001245,KF790408:0.00125):0.0):0.0,((KF886352:0.001882,(KF790438:0.000623,CY134996:0.001873):0.000623):0.001875,(KF789591:0.001879,((KF790049:0.001255,(CY134956:0.000624,CY183153:0.000624):0.000626):0.001249,((CY168407:0.004394,CY183065:0.003128):0.0,(KF598733:0.002501,((KC892174:0.0,(KF685747:0.000624,CY168471:0.000625):0.00375):0.000624,(((KC892685:0.000624,KC892641:0.0):0.001874,KC893110:0.001249):0.0,(KC892480:0.0,(JX913043:0.001249,(KF551075:0.00125,((CY114509:0.0,(KC892889:0.0,KC893018:0.002498):0.005006):0.001877,(((KC892519:0.0,KC892498:0.000624):0.002497,KC892266:0.000623):0.001026,((KC892156:0.003756,(JX978746:0.001256,KC892407:0.001883):0.001875):0.00355,((KC535402:0.000623,(KC882488:0.002498,KC535387:0.001247):0.001872):0.0,(KC535363:0.000623,((KC535396:0.000623,(KC882883:0.0,KC882867:0.000623):0.003124):0.0,((KC535378:0.001872,KC535375:0.002498):0.0,(GQ385891:0.001248,((EU779522:0.001251,(CY037727:0.0,FJ179354:0.003124):0.0):0.000623,((GQ385889:0.005007,(FJ686933:0.001243,FJ179356:0.003117):0.0):0.000622,(CY173095:0.001245,(((CY173191:0.0,CY037703:0.001247):0.000622,CY035062:0.00249):0.0,((CY173255:0.001871,(CY044748:0.0,GQ385846:0.001247):0.000623):0.0,((CY027075:0.000623,(EU199367:0.0,CY172823:0.000623):0.0):0.000623,(((CY172847:0.000623,CY025643:0.0):0.000623,CY172839:0.000623):0.001247,(((CY026251:0.002497,CY092241:0.00125):0.000624,CY026019:0.000623):0.0,((CY025341:0.002502,(CY172775:0.001247,CY172903:0.000623):0.001248):0.000622,(EU199255:0.003134,(CY172431:0.000621,((CY172223:0.003127,(CY172191:0.001254,CY020069:0.000628):0.000621):0.0,((CY092217:0.003119,(CY025485:0.001283,EU516019:0.00059):0.008843):0.001868,(CY002080:0.000622,((CY002064:0.001873,(CY002456:0.000626,CY002048:0.002491):0.001243):0.003763,(AB434109:0.006307,(((CY088198:0.001245,CY088475:0.000621):0.0,CY000257:0.000621):0.002494,((CY112957:0.003135,CY006859:0.001253):0.000616,((CY000721:0.001243,(CY114493:0.0,CY090885:0.002483):0.002488):0.0,((CY001792:0.000621,(CY001600:0.00062,CY002368:0.001865):0.0):0.0,((CY002304:0.002489,(CY006163:0.001242,CY003632:0.00062):0.0):0.00062,(CY001920:0.003739,(CY001912:0.002498,((CY001504:0.0,CY006060:0.001241):0.00062,((CY001744:0.0,CY002136:0.00124):0.00062,((CY114309:0.003746,(CY006899:0.001874,CY112901:0.001863):0.002496):0.000618,(((CY006579:0.001245,CY006283:0.000621):0.001244,CY007979:0.001864):0.0,((CY006499:0.001241,(CY006491:0.001863,CY006635:0.00124):0.0):0.00062,(((CY036847:0.002495,CY010004:0.001867):0.000621,CY012200:0.000621):0.0,(((CY010028:0.001242,CY009732:0.001242):0.0,CY010012:0.002484):0.001875,(((CY010020:0.002497,CY011416:0.001237):0.001252,CY009484:0.00062):0.005658,((CY010036:0.0,(CY039879:0.002489,CY039880:0.000621):0.002487):0.003109,((CY010628:0.000619,(CY010716:0.002485,CY010516:0.001239):0.0):0.000619,((CY012728:0.0,CY013701:0.000621):0.001243,(((CY012760:0.001239,CY013200:0.001239):0.0,CY011888:0.005614):0.0,((CY013693:0.000619,(CY012184:0.002484,CY013669:0.00124):0.00124):0.0,((CY112669:0.004353,(CY112556:0.001861,CY011896:0.000619):0.00186):0.0,(CY112605:0.001243,(CY012224:0.006953,((CY012512:0.000619,(CY012896:0.00062,CY012232:0.00062):0.000621):0.0,(CY011848:0.0,(((CY011328:0.0,CY114221:0.000619):0.001241,CY011560:0.00124):0.0,((CY012456:0.000619,CY011824:0.00124):0.0,CY017283:0.000619):0.0):0.0):0.0):0.002439):0.008263):0.000618):0.0):0.0):0.000617):0.012609):0.000619):0.001215):0.003782):0.000613):0.006878):0.0):0.001862):0.0):0.0):0.001863):0.001862):0.001245):0.0):0.001241):0.021084):0.000623):0.00065):0.003713):0.002495):0.0):0.005637):0.00313):0.002515):0.001876):0.0):0.000623):0.0):0.003749):0.0):0.0):0.000623):0.000623):0.001872):0.002503):0.0):0.0):0.000623):0.001468):0.00189):0.002721):0.002524):0.0):0.000624):0.0):0.0):0.0):0.000623):0.001248):0.001255):0.000619):0.0):0.0):0.0):0.000623):0.0):0.0):0.0):0.0;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/messages.log Tue Feb 12 08:53:39 2019 -0500 @@ -0,0 +1,633 @@ + +Loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Loaded 'IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf +Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Loaded 'convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf +Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf +Loaded 'libv3/models/codon/MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf +Loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf +Loaded '../tasks/genetic_code.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf +Loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf +Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf +Loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf +Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf +Loaded 'GrabBag' from /usr/local/lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf +Overwritten previously defined function:'_sortStringsAux' +Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Loaded 'model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf +Already loaded 'DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf +Already loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf +Already loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf +Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf +Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf +Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf +Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Loaded 'libv3/tasks/estimators.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf +Already loaded '../models/model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf +Loaded '../models/DNA/GTR.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf +Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf +Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf +Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf +Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf +Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Loaded 'libv3/tasks/alignments.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf +Already loaded '../IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf +Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Loaded 'libv3/tasks/trees.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf +Already loaded '../IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf +Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf +Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Loaded 'TreeTools' from /usr/local/lib/hyphy/TemplateBatchFiles/TreeTools.ibf +Loaded 'modules/io_functions.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf +Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf +Already loaded 'libv3/convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf +Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Loaded 'modules/selection_lib.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf +Loaded 'libv3/models/codon/BS_REL.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf +Already loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf +Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf +Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf +Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf +Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Already loaded 'MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf +Loaded '../../convenience/math.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf +Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Already loaded 'libv3/convenience/math.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf +Loaded 'libv3/tasks/mpi.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf +Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +Already loaded '../models/parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf +Variable 'NORMALIZE_SEQUENCE_NAMES' was not initialized prior to being used +Variable 'ASSUME_REVERSIBLE_MODELS' was not initialized prior to being used +Loaded 'modules/shared-load-file.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf +Variable 'MARKDOWN_OUTPUT' was not initialized prior to being used +Already loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf +Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +Variable 'JOYpYPkv.skipCodeSelectionStep' was not initialized prior to being used +Row and/or column partition is empty. All the data will be used by default. +Variable 'NEXUS_FILE_TREE_MATRIX' was not initialized prior to being used +Variable 'utility.ToggleEnvVariable.cache' was not initialized prior to being used +Variable 'TREE_NODE_NAME_MAPPING' was not initialized prior to being used +Variable '_thZqV_F.PROMPT_FOR_FILE' was not initialized prior to being used +Variable 'END_OF_FILE' was not initialized prior to being used +Variable '_DO_TREE_REBALANCE_' was not initialized prior to being used +Variable '_KEEP_I_LABELS_' was not initialized prior to being used +Variable 'INCLUDE_MODEL_SPECS' was not initialized prior to being used +Variable 'utility.ForEachPair.warn_non_rentrant' was not initialized prior to being used +Row and/or column partition is empty. All the data will be used by default. +Row and/or column partition is empty. All the data will be used by default. +Loaded 'modules/grid_compute.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf +Variable 'QPmholqs.cache' was not initialized prior to being used +Row and/or column partition is empty. All the data will be used by default. +Variable 'COUNT_GAPS_IN_FREQUENCIES' was not initialized prior to being used +Variable 'MiVdxtWn.model_pi' was not initialized prior to being used +Model MiVdxtWn.model assigned to Pig +Model MiVdxtWn.model assigned to Cow +Model MiVdxtWn.model assigned to Node3 +Model MiVdxtWn.model assigned to Horse +Model MiVdxtWn.model assigned to Cat +Model MiVdxtWn.model assigned to Node2 +Model MiVdxtWn.model assigned to RhMonkey +Model MiVdxtWn.model assigned to Baboon +Model MiVdxtWn.model assigned to Node9 +Model MiVdxtWn.model assigned to Human +Model MiVdxtWn.model assigned to Chimp +Model MiVdxtWn.model assigned to Node12 +Model MiVdxtWn.model assigned to Node8 +Model MiVdxtWn.model assigned to Node1 +Model MiVdxtWn.model assigned to Rat +Model MiVdxtWn.model assigned to Mouse +The tips of the tree:MiVdxtWn.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} + +Pseudo-optimal path's cost 2330 vs 4284 for 1..k=> a 1.83863 x improvement +Partition 0 is ASSUMED to have a reversible model +Variable 'USE_LAST_RESULTS' was not initialized prior to being used +Variable 'MiVdxtWn.tree_0.Pig.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Pig.t=0.3974535884114245 +Variable 'MiVdxtWn.tree_0.Cow.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Cow.t=0.5732857515739808 +Variable 'MiVdxtWn.tree_0.Node3.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Node3.t=0.2285810062933711 +Variable 'MiVdxtWn.tree_0.Horse.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Horse.t=0.445313802634098 +Variable 'MiVdxtWn.tree_0.Cat.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Cat.t=0.7112847618952328 +Variable 'MiVdxtWn.tree_0.Node2.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Node2.t=0.1574326532610344 +Variable 'MiVdxtWn.tree_0.RhMonkey.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.RhMonkey.t=0.00541241057687097 +Variable 'MiVdxtWn.tree_0.Baboon.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Baboon.t=0.008348273981595522 +Variable 'MiVdxtWn.tree_0.Node9.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Node9.t=0.06106219833449517 +Variable 'MiVdxtWn.tree_0.Human.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Human.t=0.01168167424258652 +Variable 'MiVdxtWn.tree_0.Chimp.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Chimp.t=0.00214616181187092 +Variable 'MiVdxtWn.tree_0.Node12.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Node12.t=0.03189158847602433 +Variable 'MiVdxtWn.tree_0.Node8.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Node8.t=0.2735913110261884 +Variable 'MiVdxtWn.tree_0.Node1.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Node1.t=0.9154145654683773 +Variable 'MiVdxtWn.tree_0.Rat.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Rat.t=0.1368762373082833 +Variable 'MiVdxtWn.tree_0.Mouse.t' was not initialized prior to being used +models.generic.SetBranchLength: MiVdxtWn.tree_0.Mouse.t=0.2630995612925615 +Variable 'MiVdxtWn.MiVdxtWn.likelihoodFunction' was not initialized prior to being used +Variable 'SAVE_OPT_STATUS_TO' was not initialized prior to being used +Set GUI update interval to every 331-th LF evaluation. +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +MiVdxtWn.model.theta_GT = 0.25 +MiVdxtWn.model.theta_CG = 0.25 +MiVdxtWn.model.theta_CT = 1 +MiVdxtWn.model.theta_AT = 0.25 +MiVdxtWn.model.theta_AC = 0.25 +MiVdxtWn.tree_0.Pig.t = 0.397454 +MiVdxtWn.tree_0.Cow.t = 0.573286 +MiVdxtWn.tree_0.Node3.t = 0.228581 +MiVdxtWn.tree_0.Horse.t = 0.445314 +MiVdxtWn.tree_0.Cat.t = 0.711285 +MiVdxtWn.tree_0.Node2.t = 0.157433 +MiVdxtWn.tree_0.RhMonkey.t = 0.00541241 +MiVdxtWn.tree_0.Baboon.t = 0.00834827 +MiVdxtWn.tree_0.Node9.t = 0.0610622 +MiVdxtWn.tree_0.Human.t = 0.0116817 +MiVdxtWn.tree_0.Chimp.t = 0.00214616 +MiVdxtWn.tree_0.Node12.t = 0.0318916 +MiVdxtWn.tree_0.Node8.t = 0.273591 +MiVdxtWn.tree_0.Node1.t = 0.915415 +MiVdxtWn.tree_0.Rat.t = 0.136876 +MiVdxtWn.tree_0.Mouse.t = 0.2631 +Optimization finished in 24 loop passes. +1467 likelihood evaluation calls and 10507 matrix exponentiations calls were made + +Variable 'BRANCH_LENGTH_STENCIL' was not initialized prior to being used +Variable 'MiVdxtWn.option' was not initialized prior to being used +Variable 'relax.terms.json.nucleotide_gtr' was not initialized prior to being used +Variable 'Unknown' was not initialized prior to being used +Variable 'SRnFPBcA.initial_value' was not initialized prior to being used +Variable 'FYuAtbni.data_filter' was not initialized prior to being used +Row and/or column partition is empty. All the data will be used by default. +Set GUI update interval to every 2879-th LF evaluation. +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +frequencies._aux.CF3x4.p0_0 = 0.415775 +frequencies._aux.CF3x4.p0_1 = 0.250343 +frequencies._aux.CF3x4.p0_2 = 0.652625 +frequencies._aux.CF3x4.p1_0 = 0.399465 +frequencies._aux.CF3x4.p1_1 = 0.28317 +frequencies._aux.CF3x4.p1_2 = 0.391304 +frequencies._aux.CF3x4.p2_0 = 0.253743 +frequencies._aux.CF3x4.p2_1 = 0.314941 +frequencies._aux.CF3x4.p2_2 = 0.521444 +Optimization finished in 5 loop passes. +184 likelihood evaluation calls and 0 matrix exponentiations calls were made + +Variable 'FYuAtbni.model_MGREV_pi' was not initialized prior to being used +Model FYuAtbni.model_MGREV assigned to Pig +Model FYuAtbni.model_MGREV assigned to Cow +Model FYuAtbni.model_MGREV assigned to Node3 +Model FYuAtbni.model_MGREV assigned to Horse +Model FYuAtbni.model_MGREV assigned to Cat +Model FYuAtbni.model_MGREV assigned to Node2 +Model FYuAtbni.model_MGREV assigned to RhMonkey +Model FYuAtbni.model_MGREV assigned to Baboon +Model FYuAtbni.model_MGREV assigned to Node9 +Model FYuAtbni.model_MGREV assigned to Human +Model FYuAtbni.model_MGREV assigned to Chimp +Model FYuAtbni.model_MGREV assigned to Node12 +Model FYuAtbni.model_MGREV assigned to Node8 +Model FYuAtbni.model_MGREV assigned to Node1 +Model FYuAtbni.model_MGREV assigned to Rat +Model FYuAtbni.model_MGREV assigned to Mouse +The tips of the tree:FYuAtbni.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} + +Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement +Partition 0 is ASSUMED to have a reversible model +Variable 'FYuAtbni.FYuAtbni.likelihoodFunction' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Pig.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Cow.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node3.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Horse.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Cat.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node2.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.RhMonkey.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Baboon.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node9.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Human.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Chimp.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node12.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node8.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node1.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Rat.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Mouse.alpha' was not initialized prior to being used +Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch +Set GUI update interval to every 187-th LF evaluation. +Initial guess for FYuAtbni.tree_0.Node2.alpha is 0.000173618 +Initial guess for FYuAtbni.tree_0.Node3.alpha is 1.15458e-05 +Initial guess for FYuAtbni.tree_0.Pig.alpha is 0.000173063 +Initial guess for FYuAtbni.tree_0.Cow.alpha is 0.000186779 +Initial guess for FYuAtbni.tree_0.Horse.alpha is 0.000174488 +Initial guess for FYuAtbni.tree_0.Cat.alpha is 0.000196799 +Initial guess for FYuAtbni.tree_0.Node8.alpha is 4.67029e-05 +Initial guess for FYuAtbni.tree_0.Node9.alpha is 0.000140119 +Initial guess for FYuAtbni.tree_0.RhMonkey.alpha is 4.64183e-06 +Initial guess for FYuAtbni.tree_0.Baboon.alpha is 1.75863e-06 +Initial guess for FYuAtbni.tree_0.Node12.alpha is 2.75759e-05 +Initial guess for FYuAtbni.tree_0.Human.alpha is 7.93383e-07 +Initial guess for FYuAtbni.tree_0.Chimp.alpha is 1.32491e-06 +Initial guess for FYuAtbni.tree_0.Rat.alpha is 8.26646e-05 +Initial guess for FYuAtbni.tree_0.Mouse.alpha is 0.000107933 +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +FYuAtbni.model_MGREV.theta_GT = 1 +FYuAtbni.model_MGREV.theta_CT = 1 +FYuAtbni.model_MGREV.theta_AC = 1 +FYuAtbni.model_MGREV.theta_CG = 1 +FYuAtbni.model_MGREV.theta_AT = 1 +FYuAtbni.model_MGREV.omega_0 = 1 +FYuAtbni.model_MGREV.omega_1 = 1 +FYuAtbni.tree_0.Pig.alpha = 0.000173063 +FYuAtbni.tree_0.Cow.alpha = 0.000186779 +FYuAtbni.tree_0.Node3.alpha = 1.15458e-05 +FYuAtbni.tree_0.Horse.alpha = 0.000174488 +FYuAtbni.tree_0.Cat.alpha = 0.000196799 +FYuAtbni.tree_0.Node2.alpha = 0.000173618 +FYuAtbni.model_MGREV.omega_2 = 1 +FYuAtbni.tree_0.RhMonkey.alpha = 4.64183e-06 +FYuAtbni.tree_0.Baboon.alpha = 1.75863e-06 +FYuAtbni.tree_0.Node9.alpha = 0.000140119 +FYuAtbni.tree_0.Human.alpha = 7.93383e-07 +FYuAtbni.tree_0.Chimp.alpha = 1.32491e-06 +FYuAtbni.tree_0.Node12.alpha = 2.75759e-05 +FYuAtbni.tree_0.Node8.alpha = 4.67029e-05 +FYuAtbni.tree_0.Node1.alpha = 0.1 +FYuAtbni.tree_0.Rat.alpha = 8.26646e-05 +FYuAtbni.tree_0.Mouse.alpha = 0.000107933 +Optimization finished in 37 loop passes. +3110 likelihood evaluation calls and 18285 matrix exponentiations calls were made + +Row and/or column partition is empty. All the data will be used by default. +Set GUI update interval to every 2926-th LF evaluation. +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +frequencies._aux.CF3x4.p0_0 = 0.415775 +frequencies._aux.CF3x4.p0_1 = 0.250343 +frequencies._aux.CF3x4.p0_2 = 0.652625 +frequencies._aux.CF3x4.p1_0 = 0.399465 +frequencies._aux.CF3x4.p1_1 = 0.28317 +frequencies._aux.CF3x4.p1_2 = 0.391304 +frequencies._aux.CF3x4.p2_0 = 0.253743 +frequencies._aux.CF3x4.p2_1 = 0.314941 +frequencies._aux.CF3x4.p2_2 = 0.521444 +Optimization finished in 5 loop passes. +184 likelihood evaluation calls and 0 matrix exponentiations calls were made + +Variable 'FYuAtbni.model_MGREV_pi' was not initialized prior to being used +Model FYuAtbni.model_MGREV assigned to Pig +Model FYuAtbni.model_MGREV assigned to Cow +Model FYuAtbni.model_MGREV assigned to Node3 +Model FYuAtbni.model_MGREV assigned to Horse +Model FYuAtbni.model_MGREV assigned to Cat +Model FYuAtbni.model_MGREV assigned to Node2 +Model FYuAtbni.model_MGREV assigned to RhMonkey +Model FYuAtbni.model_MGREV assigned to Baboon +Model FYuAtbni.model_MGREV assigned to Node9 +Model FYuAtbni.model_MGREV assigned to Human +Model FYuAtbni.model_MGREV assigned to Chimp +Model FYuAtbni.model_MGREV assigned to Node12 +Model FYuAtbni.model_MGREV assigned to Node8 +Model FYuAtbni.model_MGREV assigned to Node1 +Model FYuAtbni.model_MGREV assigned to Rat +Model FYuAtbni.model_MGREV assigned to Mouse +The tips of the tree:FYuAtbni.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} + +Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement +Partition 0 is ASSUMED to have a reversible model +Variable 'FYuAtbni.tree_0.Rat.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node1.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node8.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Cat.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node12.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Chimp.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Human.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node9.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node2.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Baboon.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.RhMonkey.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Node3.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Cow.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Pig.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Horse.alpha' was not initialized prior to being used +Variable 'FYuAtbni.tree_0.Mouse.alpha' was not initialized prior to being used +Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch +Set GUI update interval to every 285-th LF evaluation. +Initial guess for FYuAtbni.tree_0.Node2.alpha is 0.000173618 +Initial guess for FYuAtbni.tree_0.Node3.alpha is 1.15458e-05 +Initial guess for FYuAtbni.tree_0.Pig.alpha is 0.000173063 +Initial guess for FYuAtbni.tree_0.Cow.alpha is 0.000186779 +Initial guess for FYuAtbni.tree_0.Horse.alpha is 0.000174488 +Initial guess for FYuAtbni.tree_0.Cat.alpha is 0.000196799 +Initial guess for FYuAtbni.tree_0.Node8.alpha is 4.67029e-05 +Initial guess for FYuAtbni.tree_0.Node9.alpha is 0.000140119 +Initial guess for FYuAtbni.tree_0.RhMonkey.alpha is 4.64183e-06 +Initial guess for FYuAtbni.tree_0.Baboon.alpha is 1.75863e-06 +Initial guess for FYuAtbni.tree_0.Node12.alpha is 2.75759e-05 +Initial guess for FYuAtbni.tree_0.Human.alpha is 7.93383e-07 +Initial guess for FYuAtbni.tree_0.Chimp.alpha is 1.32491e-06 +Initial guess for FYuAtbni.tree_0.Rat.alpha is 8.26646e-05 +Initial guess for FYuAtbni.tree_0.Mouse.alpha is 0.000107933 +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +FYuAtbni.model_MGREV.theta_CG = 1 +FYuAtbni.model_MGREV.theta_AT = 1 +FYuAtbni.model_MGREV.theta_CT = 1 +FYuAtbni.model_MGREV.theta_GT = 1 +FYuAtbni.model_MGREV.theta_AC = 1 +FYuAtbni.model_MGREV.omega_0 = 1 +FYuAtbni.model_MGREV.omega_1 = 1 +FYuAtbni.tree_0.Pig.alpha = 0.000173063 +FYuAtbni.tree_0.Cow.alpha = 0.000186779 +FYuAtbni.tree_0.Node3.alpha = 1.15458e-05 +FYuAtbni.tree_0.Horse.alpha = 0.000174488 +FYuAtbni.tree_0.Cat.alpha = 0.000196799 +FYuAtbni.tree_0.Node2.alpha = 0.000173618 +FYuAtbni.model_MGREV.omega_2 = 1 +FYuAtbni.tree_0.RhMonkey.alpha = 4.64183e-06 +FYuAtbni.tree_0.Baboon.alpha = 1.75863e-06 +FYuAtbni.tree_0.Node9.alpha = 0.000140119 +FYuAtbni.tree_0.Human.alpha = 7.93383e-07 +FYuAtbni.tree_0.Chimp.alpha = 1.32491e-06 +FYuAtbni.tree_0.Node12.alpha = 2.75759e-05 +FYuAtbni.tree_0.Node8.alpha = 4.67029e-05 +FYuAtbni.tree_0.Node1.alpha = 0.1 +FYuAtbni.tree_0.Rat.alpha = 8.26646e-05 +FYuAtbni.tree_0.Mouse.alpha = 0.000107933 +Optimization finished in 30 loop passes. +3225 likelihood evaluation calls and 18018 matrix exponentiations calls were made + +Overwritten previously defined function:'GpmgdDcy.rate_generator' +Overwritten previously defined function:'GpmgdDcy.rate_generator' +Set GUI update interval to every 2992-th LF evaluation. +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +frequencies._aux.CF3x4.p0_0 = 0.415775 +frequencies._aux.CF3x4.p0_1 = 0.250343 +frequencies._aux.CF3x4.p0_2 = 0.652625 +frequencies._aux.CF3x4.p1_0 = 0.399465 +frequencies._aux.CF3x4.p1_1 = 0.28317 +frequencies._aux.CF3x4.p1_2 = 0.391304 +frequencies._aux.CF3x4.p2_0 = 0.253743 +frequencies._aux.CF3x4.p2_1 = 0.314941 +frequencies._aux.CF3x4.p2_2 = 0.521444 +Optimization finished in 5 loop passes. +184 likelihood evaluation calls and 0 matrix exponentiations calls were made + +Variable 'relax.test_pi' was not initialized prior to being used +Overwritten previously defined function:'GpmgdDcy.rate_generator' +Overwritten previously defined function:'GpmgdDcy.rate_generator' +Overwritten previously defined function:'GpmgdDcy.rate_generator' +Set GUI update interval to every 2912-th LF evaluation. +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +frequencies._aux.CF3x4.p0_0 = 0.415775 +frequencies._aux.CF3x4.p0_1 = 0.250343 +frequencies._aux.CF3x4.p0_2 = 0.652625 +frequencies._aux.CF3x4.p1_0 = 0.399465 +frequencies._aux.CF3x4.p1_1 = 0.28317 +frequencies._aux.CF3x4.p1_2 = 0.391304 +frequencies._aux.CF3x4.p2_0 = 0.253743 +frequencies._aux.CF3x4.p2_1 = 0.314941 +frequencies._aux.CF3x4.p2_2 = 0.521444 +Optimization finished in 5 loop passes. +184 likelihood evaluation calls and 0 matrix exponentiations calls were made + +Variable 'relax.reference_pi' was not initialized prior to being used +Overwritten previously defined function:'GpmgdDcy.rate_generator' +Overwritten previously defined function:'GpmgdDcy.rate_generator' +Overwritten previously defined function:'GpmgdDcy.rate_generator' +Set GUI update interval to every 2827-th LF evaluation. +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +frequencies._aux.CF3x4.p0_0 = 0.415775 +frequencies._aux.CF3x4.p0_1 = 0.250343 +frequencies._aux.CF3x4.p0_2 = 0.652625 +frequencies._aux.CF3x4.p1_0 = 0.399465 +frequencies._aux.CF3x4.p1_1 = 0.28317 +frequencies._aux.CF3x4.p1_2 = 0.391304 +frequencies._aux.CF3x4.p2_0 = 0.253743 +frequencies._aux.CF3x4.p2_1 = 0.314941 +frequencies._aux.CF3x4.p2_2 = 0.521444 +Optimization finished in 5 loop passes. +184 likelihood evaluation calls and 0 matrix exponentiations calls were made + +Variable 'relax.unclassified_pi' was not initialized prior to being used +No nodel was assigned to Pig +No nodel was assigned to Cow +No nodel was assigned to Node3 +No nodel was assigned to Horse +No nodel was assigned to Cat +No nodel was assigned to Node2 +No nodel was assigned to RhMonkey +No nodel was assigned to Baboon +No nodel was assigned to Node9 +No nodel was assigned to Human +No nodel was assigned to Chimp +No nodel was assigned to Node12 +No nodel was assigned to Node8 +No nodel was assigned to Node1 +No nodel was assigned to Rat +No nodel was assigned to Mouse +The tips of the tree:RPGDJipv.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} + +Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement +Partition 0 is ASSUMED to have a reversible model +relax.reference.theta_AC was already constrained in estimators.SetGlobals2 +relax.reference.theta_AG was already constrained in estimators.SetGlobals2 +relax.reference.theta_AT was already constrained in estimators.SetGlobals2 +relax.reference.theta_CG was already constrained in estimators.SetGlobals2 +relax.reference.theta_CT was already constrained in estimators.SetGlobals2 +relax.reference.theta_GT was already constrained in estimators.SetGlobals2 +relax.test.theta_AG was already constrained in estimators.SetGlobals2 +relax.unclassified.theta_AC was already constrained in estimators.SetGlobals2 +relax.unclassified.theta_AG was already constrained in estimators.SetGlobals2 +relax.unclassified.theta_AT was already constrained in estimators.SetGlobals2 +relax.unclassified.theta_CG was already constrained in estimators.SetGlobals2 +relax.unclassified.theta_CT was already constrained in estimators.SetGlobals2 +relax.unclassified.theta_GT was already constrained in estimators.SetGlobals2 +Variable 'RPGDJipv.tree_id_0.Pig.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Pig.t=1.375151388677762 +Variable 'RPGDJipv.tree_id_0.Cow.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Cow.t=1.781953803671641 +Variable 'RPGDJipv.tree_id_0.Node3.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node3.t=0.7179600319187995 +Variable 'RPGDJipv.tree_id_0.Horse.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Horse.t=1.501071819834825 +Variable 'RPGDJipv.tree_id_0.Cat.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Cat.t=1.973271183104609 +Variable 'RPGDJipv.tree_id_0.Node2.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node2.t=0.4461859649428869 +Variable 'RPGDJipv.tree_id_0.RhMonkey.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.RhMonkey.t=0.02655846610185887 +Variable 'RPGDJipv.tree_id_0.Baboon.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Baboon.t=0.01259838399210765 +Variable 'RPGDJipv.tree_id_0.Node9.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node9.t=0.1891887653227436 +Variable 'RPGDJipv.tree_id_0.Human.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Human.t=0 +Variable 'RPGDJipv.tree_id_0.Chimp.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Chimp.t=0.01302152547854442 +Variable 'RPGDJipv.tree_id_0.Node12.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node12.t=0.1235892304460588 +Variable 'RPGDJipv.tree_id_0.Node8.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node8.t=0.8108545924902142 +Variable 'RPGDJipv.tree_id_0.Node1.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node1.t=2.056868575380766 +Variable 'RPGDJipv.tree_id_0.Rat.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Rat.t=0.485173250741015 +Variable 'RPGDJipv.tree_id_0.Mouse.t' was not initialized prior to being used +models.generic.SetBranchLength: RPGDJipv.tree_id_0.Mouse.t=0.8522851263393678 +Variable 'RPGDJipv.RPGDJipv.likelihoodFunction' was not initialized prior to being used +Set GUI update interval to every 26-th LF evaluation. +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +relax.test.theta_GT = 0.315401 +relax.test.theta_CT = 0.98654 +relax.test.theta_AC = 0.578523 +relax.test.theta_CG = 0.469908 +relax.test.theta_AT = 0.267066 +relax.reference.bsrel_mixture_aux_1 = 0.818182 +relax.reference.omega1 = 0.145496 +relax.reference.omega2 = 0.4601 +relax.reference.bsrel_mixture_aux_0 = 0.45 +relax.reference.omega3 = 7.27482 +relax.unclassified.omega3 = 1 +relax.unclassified.bsrel_mixture_aux_1 = 0.5 +relax.unclassified.omega2 = 1 +relax.unclassified.omega1 = 1 +relax.K = 1 +relax.unclassified.bsrel_mixture_aux_0 = 0.5 +RPGDJipv.tree_id_0.Pig.t = 1.37515 +RPGDJipv.tree_id_0.Cow.t = 1.78195 +RPGDJipv.tree_id_0.Node3.t = 0.71796 +RPGDJipv.tree_id_0.Horse.t = 1.50107 +RPGDJipv.tree_id_0.Cat.t = 1.97327 +RPGDJipv.tree_id_0.Node2.t = 0.446186 +RPGDJipv.tree_id_0.RhMonkey.t = 0.0265585 +RPGDJipv.tree_id_0.Baboon.t = 0.0125984 +RPGDJipv.tree_id_0.Node9.t = 0.189189 +RPGDJipv.tree_id_0.Human.t = 0 +RPGDJipv.tree_id_0.Chimp.t = 0.0130215 +RPGDJipv.tree_id_0.Node12.t = 0.123589 +RPGDJipv.tree_id_0.Node8.t = 0.810855 +RPGDJipv.tree_id_0.Node1.t = 2.05687 +RPGDJipv.tree_id_0.Rat.t = 0.485173 +RPGDJipv.tree_id_0.Mouse.t = 0.852285 +Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch +Optimization finished in 156 loop passes. +19208 likelihood evaluation calls and 408312 matrix exponentiations calls were made + +Variable 'MPI_NODE_COUNT' was not initialized prior to being used +Variable 'esPQwqFL.RPGDJipv.likelihoodFunction' was not initialized prior to being used +Set GUI update interval to every 24-th LF evaluation. +Optimization settings: + OPTIMIZATION_METHOD = 4 + OPTIMIZATION_PRECISION = 0.001 + MAXIMUM_ITERATIONS_PER_VARIABLE = 5000 + +Initial parameter values + +relax.test.theta_GT = 0.272534 +relax.test.theta_CT = 0.989376 +relax.test.theta_AC = 0.472659 +relax.test.theta_CG = 0.409729 +relax.test.theta_AT = 0.213063 +relax.reference.omega2 = 0 +relax.reference.omega3 = 1.81261 +relax.reference.bsrel_mixture_aux_1 = 0.398417 +relax.reference.bsrel_mixture_aux_0 = 0.26934 +relax.reference.omega1 = 0 +relax.unclassified.omega2 = 3.8108 +relax.unclassified.bsrel_mixture_aux_1 = 0.965815 +relax.unclassified.omega3 = 88.0589 +relax.unclassified.omega1 = 0 +relax.unclassified.bsrel_mixture_aux_0 = 0.488814 +RPGDJipv.tree_id_0.Pig.t = 0.288673 +RPGDJipv.tree_id_0.Cow.t = 0.415456 +RPGDJipv.tree_id_0.Node3.t = 0.165342 +RPGDJipv.tree_id_0.Horse.t = 0.373597 +RPGDJipv.tree_id_0.Cat.t = 0.4862 +RPGDJipv.tree_id_0.Node2.t = 0.071002 +RPGDJipv.tree_id_0.RhMonkey.t = 0.0109335 +RPGDJipv.tree_id_0.Baboon.t = 0.00559127 +RPGDJipv.tree_id_0.Node9.t = 0.0891892 +RPGDJipv.tree_id_0.Human.t = 0 +RPGDJipv.tree_id_0.Chimp.t = 0.0054891 +RPGDJipv.tree_id_0.Node12.t = 0.0161348 +RPGDJipv.tree_id_0.Node8.t = 0.405701 +RPGDJipv.tree_id_0.Node1.t = 1.12055 +RPGDJipv.tree_id_0.Rat.t = 0.217643 +RPGDJipv.tree_id_0.Mouse.t = 0.392946 +Optimization finished in 62 loop passes. +6270 likelihood evaluation calls and 146691 matrix exponentiations calls were made + +Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used \ No newline at end of file
--- a/test-data/relax-in1.nhx Mon Feb 11 20:18:43 2019 -0500 +++ b/test-data/relax-in1.nhx Tue Feb 12 08:53:39 2019 -0500 @@ -1,1 +1,1 @@ -((((Pig{FG}:0.147969,Cow{TEST}:0.21343):0.085099,Horse{TEST}:0.165787,Cat{TEST}:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108){REFERENCE}:0.022733,(Human:0.004349,Chimp:0.000799){REFERENCE}:0.011873){REFERENCE}:0.101856):0.340802,Rat:0.050958,Mouse:0.09795) \ No newline at end of file +((((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Horse{TEST}:0.165787,Cat{TEST}:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.09795) \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nhx Tue Feb 12 08:53:39 2019 -0500 @@ -0,0 +1,1 @@ +((((Pig{TEST}:0.147969,Cow{TEST}:0.21343){TEST}:0.085099,Horse:0.165787,Cat:0.264806){TEST}:0.058611,((RhMonkey{REFERENCE}:0.002015,Baboon{REFERENCE}:0.003108){REFERENCE}:0.022733,(Human{REFERENCE}:0.004349,Chimp{REFERENCE}:0.000799):0.011873){REFERENCE}:0.101856){REFERENCE}:0.340802,Rat{REFERENCE}:0.050958,Mouse{REFERENCE}:0.09795)
--- a/test-data/relax-out1.json Mon Feb 11 20:18:43 2019 -0500 +++ b/test-data/relax-out1.json Tue Feb 12 08:53:39 2019 -0500 @@ -8,7 +8,7 @@ "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)" }, "input":{ - "file name":"/Users/ryanvelazquez/Documents/misc/galaxy items/tools-iuc/tools/hyphy/test-data/relax-in1.fa", + "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa", "number of sequences":10, "number of sites":187, "partition count":1, @@ -38,9 +38,9 @@ "display order":0 }, "MG94xREV with separate rates for branch sets":{ - "Log Likelihood":-3458.097783887836, - "estimated parameters":33, - "AIC-c":6983.417789997894, + "Log Likelihood":-3460.931903299487, + "estimated parameters":32, + "AIC-c":6987.013507197776, "Equilibrium frequencies":[ [0.04785168648208005], [0.03911346079312019], @@ -106,131 +106,194 @@ ], "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *Reference*":[ - [0.5998337130511077, 1] + [1.617765969026557, 1] ], "non-synonymous/synonymous rate ratio for *Test*":[ - [1.554836363231672, 1] - ], - "non-synonymous/synonymous rate ratio for *Unclassified*":[ - [1.323008542237338, 1] + [0.7687683974183303, 1] ] }, "display order":1 }, + "General descriptive":{ + "Log Likelihood":-3420.975369746331, + "estimated parameters":51, + "AIC-c":6946.868231241836, + "Rate Distributions":{ + "Shared":{ + "0":{ + "omega":1e-08, + "proportion":0.2345034364701236 + }, + "1":{ + "omega":1e-08, + "proportion":0.3180344596999608 + }, + "2":{ + "omega":6.64943557055033, + "proportion":0.4474621038299156 + } + } + }, + "display order":4 + }, "RELAX alternative":{ - "Log Likelihood":-3427.641466344699, - "estimated parameters":41, - "AIC-c":6939.166958947604, + "Log Likelihood":-3429.125323833579, + "estimated parameters":36, + "AIC-c":6931.704002822642, "Rate Distributions":{ "Test":{ "0":{ "omega":0, - "proportion":0.2911071539848986 + "proportion":0.1993913071931658 }, "1":{ "omega":0, - "proportion":0.2693397808592169 + "proportion":0.3360341729181165 }, "2":{ - "omega":5.424306690747749, - "proportion":0.4395530651558845 + "omega":2.153056268947235, + "proportion":0.4645745198887177 } }, "Reference":{ "0":{ "omega":0, - "proportion":0.2911071539848986 + "proportion":0.1993913071931658 }, "1":{ "omega":0, - "proportion":0.2693397808592169 + "proportion":0.3360341729181165 }, "2":{ - "omega":1.812613591933097, - "proportion":0.4395530651558845 + "omega":6.166712663934246, + "proportion":0.4645745198887177 } } }, "display order":2 }, "RELAX null":{ - "Log Likelihood":-3434.619492705835, - "estimated parameters":40, - "AIC-c":6951.032315100023, + "Log Likelihood":-3437.187429488768, + "estimated parameters":35, + "AIC-c":6945.748904779063, "Rate Distributions":{ "Test":{ "0":{ - "omega":0.1293481638748959, - "proportion":0.4017058334895309 + "omega":0.1177689533662908, + "proportion":0.4926494715348529 }, "1":{ - "omega":0.2021540589664449, - "proportion":0.2729236995381347 + "omega":0.3195682613972807, + "proportion":0.1517366025099117 }, "2":{ - "omega":3.767190802229909, - "proportion":0.3253704669723343 + "omega":3.893733071412322, + "proportion":0.3556139259552353 } }, "Reference":{ "0":{ - "omega":0.1293481638748959, - "proportion":0.4017058334895309 + "omega":0.1177689533662908, + "proportion":0.4926494715348529 }, "1":{ - "omega":0.2021540589664449, - "proportion":0.2729236995381347 + "omega":0.3195682613972807, + "proportion":0.1517366025099117 }, "2":{ - "omega":3.767190802229909, - "proportion":0.3253704669723343 + "omega":3.893733071412322, + "proportion":0.3556139259552353 } } }, "display order":3 + }, + "RELAX partitioned descriptive":{ + "Log Likelihood":-3427.515821600644, + "estimated parameters":40, + "AIC-c":6936.824972889643, + "Rate Distributions":{ + "Test":{ + "0":{ + "omega":0.2264899618249929, + "proportion":0.1370778077745601 + }, + "1":{ + "omega":0.2328054750512875, + "proportion":0.6322930022247097 + }, + "2":{ + "omega":4.13407071706127, + "proportion":0.2306291900007301 + } + }, + "Reference":{ + "0":{ + "omega":0, + "proportion":0.09054841512283768 + }, + "1":{ + "omega":0, + "proportion":0.4231976237742962 + }, + "2":{ + "omega":5.975493863572218, + "proportion":0.4862539611028661 + } + } + }, + "display order":5 } }, "timers":{ "Overall":{ - "timer":313, + "timer":562, "order":0 }, "Preliminary model fitting":{ - "timer":17, + "timer":33, "order":1 }, + "General descriptive model fitting":{ + "timer":256, + "order":2 + }, "RELAX alternative model fitting":{ - "timer":190, + "timer":78, "order":3 }, "RELAX null model fitting":{ - "timer":56, + "timer":98, "order":4 + }, + "RELAX partitioned descriptive":{ + "timer":95, + "order":5 } }, "test results":{ - "LRT":13.95605272227021, - "p-value":0.0001871341719564823, - "relaxation or intensification parameter":2.842932101048393 + "LRT":16.12421131037809, + "p-value":5.932080525117289e-05, + "relaxation or intensification parameter":0.4215604262166031 }, "tested":{ "0":{ "Pig":"Test", - "Cow":"Test", + "Cow":"Reference", "Node3":"Test", - "Horse":"Unclassified", - "Cat":"Unclassified", + "Horse":"Reference", + "Cat":"Reference", "Node2":"Test", - "RhMonkey":"Reference", - "Baboon":"Reference", - "Node9":"Reference", - "Human":"Reference", - "Chimp":"Reference", - "Node12":"Unclassified", - "Node8":"Reference", - "Node1":"Reference", - "Rat":"Reference", - "Mouse":"Reference" + "RhMonkey":"Test", + "Baboon":"Test", + "Node9":"Test", + "Human":"Test", + "Chimp":"Test", + "Node12":"Test", + "Node8":"Test", + "Node1":"Test", + "Rat":"Test", + "Mouse":"Test" } }, "data partitions":{ @@ -247,107 +310,155 @@ "original name":"Human", "Nucleotide GTR":0, "MG94xREV with separate rates for branch sets":0, + "General descriptive":0, + "k (general descriptive)":0.7168352052656061, "RELAX alternative":0, - "RELAX null":0 + "RELAX null":0, + "RELAX partitioned descriptive":0 }, "Chimp":{ "original name":"Chimp", "Nucleotide GTR":0.001818722292071369, - "MG94xREV with separate rates for branch sets":0.001825814939240948, - "RELAX alternative":0.001827359202671433, - "RELAX null":0.001832714466554264 + "MG94xREV with separate rates for branch sets":0.001828056639868651, + "General descriptive":0.001850581335499795, + "k (general descriptive)":2.329184252362038, + "RELAX alternative":0.001831548027528597, + "RELAX null":0.001835680183060623, + "RELAX partitioned descriptive":0.00183255534978807 }, "Baboon":{ "original name":"Baboon", "Nucleotide GTR":0.001682319705247233, - "MG94xREV with separate rates for branch sets":0.001766484099039326, - "RELAX alternative":0.001861371759740878, - "RELAX null":0.001880673658452964 + "MG94xREV with separate rates for branch sets":0.001770013551346919, + "General descriptive":0.001869883333754939, + "k (general descriptive)":0.1228116964827354, + "RELAX alternative":0.001867314836287998, + "RELAX null":0.001853697678697539, + "RELAX partitioned descriptive":0.00189422569191071 }, "RhMonkey":{ "original name":"RhMonkey", "Nucleotide GTR":0.003776495523121213, - "MG94xREV with separate rates for branch sets":0.003723898882047009, - "RELAX alternative":0.003639853124053051, - "RELAX null":0.003643307484186126 + "MG94xREV with separate rates for branch sets":0.003720554271464007, + "General descriptive":0.003663070393385353, + "k (general descriptive)":2.272939790126477, + "RELAX alternative":0.003641537789305734, + "RELAX null":0.003670955010908306, + "RELAX partitioned descriptive":0.003632158699516803 }, "Cow":{ "original name":"Cow", "Nucleotide GTR":0.2483201583381086, - "MG94xREV with separate rates for branch sets":0.2498568912791163, - "RELAX alternative":0.3277677731077431, - "RELAX null":0.2925738796283687 + "MG94xREV with separate rates for branch sets":0.2522875145085426, + "General descriptive":0.3735091756053704, + "k (general descriptive)":1.19957642031092, + "RELAX alternative":0.3407703477665083, + "RELAX null":0.2958310860090909, + "RELAX partitioned descriptive":0.3460604457589064 }, "Pig":{ "original name":"Pig", "Nucleotide GTR":0.1871417867164377, - "MG94xREV with separate rates for branch sets":0.1928170361685192, - "RELAX alternative":0.2277442542245479, - "RELAX null":0.2135004206466554 + "MG94xREV with separate rates for branch sets":0.1903173961963296, + "General descriptive":0.2109384940367451, + "k (general descriptive)":0.6656155688777629, + "RELAX alternative":0.197167672065417, + "RELAX null":0.2182629931612711, + "RELAX partitioned descriptive":0.2076369268997903 }, "Horse":{ "original name":"Horse", "Nucleotide GTR":0.2091567334932583, - "MG94xREV with separate rates for branch sets":0.2104729862905725, - "RELAX alternative":0.4059233413351091, - "RELAX null":0.3765897594433346 + "MG94xREV with separate rates for branch sets":0.2159358728261337, + "General descriptive":0.2810540078141565, + "k (general descriptive)":0.8115699858212525, + "RELAX alternative":0.3032889682089364, + "RELAX null":0.2571098559672552, + "RELAX partitioned descriptive":0.3026705354406338 }, "Cat":{ "original name":"Cat", "Nucleotide GTR":0.2660040109418023, - "MG94xREV with separate rates for branch sets":0.276682483263765, - "RELAX alternative":0.5282692675142623, - "RELAX null":0.4799690800516377 + "MG94xREV with separate rates for branch sets":0.2795692100037539, + "General descriptive":0.3635335087937213, + "k (general descriptive)":0.9728289997736356, + "RELAX alternative":0.3660889485578829, + "RELAX null":0.3281803512051322, + "RELAX partitioned descriptive":0.370631318143086 }, "Mouse":{ "original name":"Mouse", "Nucleotide GTR":0.1182531454610134, - "MG94xREV with separate rates for branch sets":0.1195032731554601, - "RELAX alternative":0.1308145806782354, - "RELAX null":0.1470888073398289 + "MG94xREV with separate rates for branch sets":0.1199409901922202, + "General descriptive":0.1313354563273305, + "k (general descriptive)":0.2294495132372282, + "RELAX alternative":0.1341640738853253, + "RELAX null":0.1483938193994467, + "RELAX partitioned descriptive":0.1476318125310598 }, "Rat":{ "original name":"Rat", "Nucleotide GTR":0.06669544716210057, - "MG94xREV with separate rates for branch sets":0.06802863234285669, - "RELAX alternative":0.07245491834414142, - "RELAX null":0.07477863103169577 + "MG94xREV with separate rates for branch sets":0.06725647453745125, + "General descriptive":0.07175915155128718, + "k (general descriptive)":0.5208088414555363, + "RELAX alternative":0.0724007498013708, + "RELAX null":0.07365614414375878, + "RELAX partitioned descriptive":0.07568744563050285 }, "Node1":{ "Nucleotide GTR":0.2771601504028877, - "MG94xREV with separate rates for branch sets":0.2884041028198522, - "RELAX alternative":0.3730383578090298, - "RELAX null":0.451812176248499 + "MG94xREV with separate rates for branch sets":0.286127507474972, + "General descriptive":0.3532216661512288, + "k (general descriptive)":0.2199586786715634, + "RELAX alternative":0.3833004811985787, + "RELAX null":0.4576044234710181, + "RELAX partitioned descriptive":0.4360897576025625 }, "Node12":{ "Nucleotide GTR":0.01783222754921504, - "MG94xREV with separate rates for branch sets":0.01732908050208956, - "RELAX alternative":0.01753088629189957, - "RELAX null":0.01907243110988959 + "MG94xREV with separate rates for branch sets":0.01799298835381691, + "General descriptive":0.01771170858901891, + "k (general descriptive)":0.1560499010177516, + "RELAX alternative":0.01833338832069913, + "RELAX null":0.01828012634520382, + "RELAX partitioned descriptive":0.01877701767421286 }, "Node2":{ "Nucleotide GTR":0.06619118337434968, - "MG94xREV with separate rates for branch sets":0.06256202484222494, - "RELAX alternative":0.0560159229945103, - "RELAX null":0.05930942174393248 + "MG94xREV with separate rates for branch sets":0.06192085035608558, + "General descriptive":0.05843310574046084, + "k (general descriptive)":0.2816499194095207, + "RELAX alternative":0.05469841675490748, + "RELAX null":0.06219694236954142, + "RELAX partitioned descriptive":0.06011281230238084 }, "Node3":{ "Nucleotide GTR":0.09883746945145887, - "MG94xREV with separate rates for branch sets":0.1006688620480881, - "RELAX alternative":0.1304440727067901, - "RELAX null":0.12356636531614 + "MG94xREV with separate rates for branch sets":0.09744342239018626, + "General descriptive":0.1340338084149808, + "k (general descriptive)":0.8358980179450297, + "RELAX alternative":0.1164056814082033, + "RELAX null":0.1282588343299434, + "RELAX partitioned descriptive":0.1194563668460339 }, "Node8":{ "Nucleotide GTR":0.106110061225871, - "MG94xREV with separate rates for branch sets":0.1136940853020744, - "RELAX alternative":0.1350606162092146, - "RELAX null":0.1366048365485918 + "MG94xREV with separate rates for branch sets":0.1090208137603471, + "General descriptive":0.1401594332730181, + "k (general descriptive)":0.9135621448569878, + "RELAX alternative":0.1275155316795084, + "RELAX null":0.1346842719904758, + "RELAX partitioned descriptive":0.1358683972849559 }, "Node9":{ "Nucleotide GTR":0.02567391471029082, - "MG94xREV with separate rates for branch sets":0.02652712807205039, - "RELAX alternative":0.02969171453244129, - "RELAX null":0.02893959719634103 + "MG94xREV with separate rates for branch sets":0.02582385148170195, + "General descriptive":0.02665352479510937, + "k (general descriptive)":0.1089752436854629, + "RELAX alternative":0.02681134359856903, + "RELAX null":0.02759760291393045, + "RELAX partitioned descriptive":0.02746061131173372 } }, "attributes":{ @@ -363,6 +474,14 @@ "attribute type":"branch length", "display order":1 }, + "General descriptive":{ + "attribute type":"branch length", + "display order":4 + }, + "k (general descriptive)":{ + "attribute type":"branch label", + "display order":4 + }, "RELAX alternative":{ "attribute type":"branch length", "display order":2 @@ -370,6 +489,10 @@ "RELAX null":{ "attribute type":"branch length", "display order":3 + }, + "RELAX partitioned descriptive":{ + "attribute type":"branch length", + "display order":5 } } }