[general] datafname = clover_moreSpecies_medicagoOut.nex constraintfile = none streefname = stepwise attachmentspertaxon = 50 ofprefix = clover_updated.GTRpG randseed = -1 availablememory = 512 logevery = 10 saveevery = 100 refinestart = 1 outputeachbettertopology = 0 outputcurrentbesttopology = 0 enforcetermconditions = 1 genthreshfortopoterm = 20000 scorethreshforterm = 0.05 significanttopochange = 0.01 outputphyliptree = 0 outputmostlyuselessfiles = 0 writecheckpoints = 0 restart = 0 outgroup = 1 resampleproportion = 1.0 inferinternalstateprobs = 0 outputsitelikelihoods = 0 optimizeinputonly = 0 collapsebranches = 1 searchreps = 10 bootstrapreps = 0 [model1] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none [master] nindivs = 4 holdover = 1 selectionintensity = 0.5 holdoverpenalty = 0 stopgen = 5000000 stoptime = 5000000 startoptprec = 0.5 minoptprec = 0.01 numberofprecreductions = 10 treerejectionthreshold = 50.0 topoweight = 1.0 modweight = 0.05 brlenweight = 0.2 randnniweight = 0.1 randsprweight = 0.3 limsprweight = 0.6 intervallength = 100 intervalstostore = 5 limsprrange = 6 meanbrlenmuts = 5 gammashapebrlen = 1000 gammashapemodel = 1000 uniqueswapbias = 0.1 distanceswapbias = 1.0