StartService=recidcm3;
suppressDialogs=true;
StartCommandObject;
<?xml version="1.0" encoding="UTF-8"?>
<command-object>
<command-target>
<reference />
<ui-id></ui-id>
</command-target>
<commands>
NexusOpen=share/cipres/help/sampleFiles/TestNexusFile.nex;
</commands>
<commands>
SetStartingTreeInferenceModule=location_placeholder,IDL:CipresIDL_api1/TreeInfer:1.0,paup,Python wrapper around PAUP's HSearch command (using parsimony). file-based io.
</commands>
<commands>
SetMaxTaxaSubsetSize=20;
</commands>
<commands>
SetMaxIterations=2;
</commands>
<commands>
SetTreeDecompModule=location_placeholder,IDL:CipresIDL_api1/TreeDecompose:1.0,dcm3,Roshan DCM
</commands>
<commands>
SetLargeTreeInferenceModule=location_placeholder,IDL:CipresIDL_api1/TreeImprove:1.0,paup,Python wrapper around PAUP's HSearch command (using parsimony). file-based io.
</commands>
<commands>
SetSmallTreeInferenceModule=location_placeholder,IDL:CipresIDL_api1/TreeImprove:1.0,paup,Python wrapper around PAUP's HSearch command (using parsimony). file-based io.
</commands>
<commands>
SetTreeRefineModule=location_placeholder,IDL:CipresIDL_api1/TreeRefine:1.0,PIPRes_random_refine,Python implementation of a random refinement of polytomies (Random seed hard-coded for debugging purposes)
</commands>
<commands>
SetTreeMergeModule=location_placeholder,IDL:CipresIDL_api1/TreeMerge:1.0,phycas,C++ implementation of SCM (Yu Fan and Paul Lewis)
</commands>
<children>
<command-target>
<reference />
<ui-id>
StartingTreeInferenceModule
</ui-id>
</command-target>
<commands>
SetStartingTreeInferenceServiceCommmand= set Increase=Auto; set AutoInc=100; Default HS addseq=random swap=spr multrees=no timelimit=None reconlimit=Infinity;
</commands>
</children>
<children>
<command-target>
<reference />
<ui-id>
LargeTreeInferenceModule
</ui-id>
</command-target>
<commands>
SetLargeTreeInferenceServiceCommmand= set Increase=Auto; set AutoInc=100; Default HS swap=tbr multrees=no timelimit=None reconlimit=Infinity;
</commands>
</children>
<children>
<command-target>
<reference />
<ui-id>
SmallTreeInferenceModule
</ui-id>
</command-target>
<commands>
SetSmallTreeInferenceServiceCommmand= set Increase=Auto; set AutoInc=100; Default HS swap=tbr multrees=no timelimit=None reconlimit=Infinity;
</commands>
</children>
</command-object>
EndCommandObject;
LaunchService;
SaveResultsFile=TestResultsTest.txt;
EndService;