[general]
invariantsites = estimate
numratecats = 4
ratehetmodel = gamma
streefname = random
datatype = nucleotide
searchreps=2
statefrequencies = estimate
ratematrix = 6rate
numratecats=4
restart = 0
saveevery = 100
ofprefix = garli_run
enforcetermconditions = 1
genthreshfortopoterm = 10000
significanttopochange = 0.01
scorethreshforterm = 0.05
logevery = 10
datafname = infile
outputeachbettertopology = 0
outputphyliptree = 0
availablememory = 2560
outputmostlyuselessfiles = 0
writecheckpoints = 0
refinestart = 1
randseed = -1
constraintfile = none
[master]
treerejectionthreshold = 50.0
gammashapemodel = 1000
meanbrlenmuts = 5
holdoverpenalty = 0
limsprrange= 6
uniqueswapbias = 0.1
distanceswapbias = 1.0
stopgen = 214783646
stoptime = 214783646
bootstrapreps = 0
resampleproportion = 1.0
startoptprec = 0.5
minoptprec = 0.01
numberofprecreductions = 20
selectionintensity = 0.5
nindivs = 4
holdover = 1
inferinternalstateprobs = 0
intervallength = 100
gammashapebrlen = 1000
modweight = 0.05
brlenweight = 0.2
topoweight = 1.0
randnniweight = 0.1
randsprweight = 0.3
limsprweight = 0.6
intervalstostore = 5