Hello,
I seem to be having issues with convergence in my Bayesian analysis. I'm using a single gene large dataset of 418 individuals. My PSFR values say N/A in my output but my split frequency is 0.007. Also, my consensus tree gives me posterior probabilities of 0.5 or 1 with no distnguishable clades (see attached). Below is my Bayes block:
begin mrbayes;
charset F_1 = 1 - 655\3;
charset F_2 = 2 - 656\3;
charset F_3 = 3 - 657\3;
partition currentPartition = 3: F_1, F_2, F_3;
set partition = currentPartition;
lset applyto=(1) nst=6 rates=gamma;
lset applyto=(2) nst=2 rates=invgamma;
lset applyto=(3) nst=6 rates=gamma;
unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);
prset applyto=(all) ratepr=variable;
mcmc ngen= 24000000 append=yes samplefreq=1000 nchains=8;
sump burnin = 10000;
sumt burnin = 10000;
end;
Any advice? Thanks!
You have a fairly larger dataset so I would try with more generation time. On other hand I would check a modeltest for the 1st and 2nd as often they have the same model when tested (I don't have much experience but that is what I have seen).
I am not sure you need to you need to unlink the 3 partition and then set the priors as variable. Have you tried to remove:
unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);
prset applyto=(all) ratepr=variable;
Finally, I don't see in the code where do you set the 2 independent runs (nrun=Number or independent analysis with the same dataset and script) so I guess you run 8 chains but in a single run. So how come they don't converge? All the chains are dependent.
Try to add nrun=2 [usual for Bayesian] each run has 4 chains by default so no need to set that up.
mcmc ngen= 24000000 append=yes samplefreq=1000 nrun=2;
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