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[general]
datafname = zakonEtAl2006.11tax.nex
constraintfile = none
streefname = stepwise
attachmentspertaxon = 50
ofprefix = codon.GY94.F3x4
randseed = -1
availablememory = 512
logevery = 10
saveevery = 100
refinestart = 1
outputeachbettertopology = 0
outputcurrentbesttopology = 0
enforcetermconditions = 1
genthreshfortopoterm = 2000
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 = 2
bootstrapreps = 0
[model1]
datatype = codon
geneticcode = standard
ratematrix = 2rate
statefrequencies = f3x4
ratehetmodel = none
numratecats = 1
invariantsites = none
[master]
nindivs = 4
holdover = 1
selectionintensity = 0.5
holdoverpenalty = 0
stopgen = 5000000
stoptime = 5000000
startoptprec = 0.5
minoptprec = 0.01
numberofprecreductions = 1
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
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