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[general]
datafname = data/z.byPos.11x2178.nex
constraintfile = none
streefname = data/p.3diff.start
attachmentspertaxon = 50
ofprefix = ch.p.3diff
randseed = -1
availablememory = 512
logevery = 10
saveevery = 100
refinestart = 1
refineend = 0
outputeachbettertopology = 0
outputcurrentbesttopology = 0
enforcetermconditions = 1
genthreshfortopoterm = 5000
scorethreshforterm = 0.001
significanttopochange = 0.01
outputphyliptree = 0
outputmostlyuselessfiles = 0
writecheckpoints = 0
restart = 1
usepatternmanager = 1
searchreps = 1
collapsebranches = 1
linkmodels = 0
subsetspecificrates = 1
[model1]
datatype = nucleotide
ratematrix = ( 0 1 2 2 3 4 )
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = none
[model2]
datatype = nucleotide
ratematrix = ( 0 1 2 1 0 3 )
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = none
[model3]
datatype = nucleotide
ratematrix = ( 0 1 2 3 1 0 )
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate
[master]
nindivs = 4
holdover = 1
selectionintensity = 0.5
holdoverpenalty = 0
stopgen = 2000
stoptime = 1
startoptprec = 0.5
minoptprec = 0.01
numberofprecreductions = 5
treerejectionthreshold = 50.0
topoweight = 0.01
modweight = 0.002
brlenweight = 0.002
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
bootstrapreps = 1
resampleproportion = 1.0
inferinternalstateprobs = 0
|
