set autoclose=yes
set nowarnings=yes
execute infile.nex
log start filename=mrbayeslog.out append
lset coding = all
lset Nucmodel= 4by4
lset Nst= 1
lset Rates= equal
lset Nbetacat= 5
prset brlenspr = unconstrained:exponential(10.0)
prset Tratiopr = beta(1.0, 1.0)
prset covswitchpr = uniform(0.0,100.0)
prset statefreqpr = dirichlet(1.0)
prset ratecorrpr = uniform(-1.0,1.0)
prset ratepr = fixed
prset pinvarpr = uniform(0.0,1.0)
prset revmatpr = dirichlet(1.0,1.0,1.0,1.0,1.0,1.0)
report revmat=dir
report Siterates=No
mcmc ngen=1000 filename=infile.nex seed=1116355510 swapseed=1116355510 nruns=2 nchains=4 temp=0.200  swapfreq=1 nswaps=1 samplefreq=1000 mcmcdiagn=Yes minpartfreq=0.1 allchains=No relburnin=Yes burnin=0 burninfrac=0.25 stoprule=Yes startingtree=random stopval=0.01 Savebrlens=Yes nperts=0 Ordertaxa=Yes
sump burnin=0 nruns=1 printtofile=yes outputname=sumpoutput.out plot=Yes marglike=Yes table=Yes
sumt burnin=0 nruns=2 ntrees=1 displaygeq=0.05 contype=Halfcompat 
quit