garli.cipres.single.conf

[general]
datafname = infile
ofprefix = garli_run
subsetspecificrates = 1
constraintfile = none
streefname = stepwise
linkmodels = 0
attachmentspertaxon = 50
randseed = -1
availablememory = 2000
logevery = 10
saveevery = 100
refinestart = 1
outputeachbettertopology = 0
outputcurrentbesttopology = 0
enforcetermconditions = 1
genthreshfortopoterm = 20000
scorethreshforterm = 0.01
significanttopochange = 0.01
outputphyliptree = 1
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 = nucleotide
ratematrix = 2rate
statefrequencies = equal
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

[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