Help with Mr Bayes parameters for 16S phylogeny

Question

[buhbs]

I am trying to construct a Bayesian analysis and phylogenetic tree using MrBayes. I have a set of 85 sequences with an alignment of about 900 bps. I am having trouble getting convergence and the analysis just keeps running. Here are my parameters. Does anyone have any ideas for different parameters that I could use to get convergence?

nst=6 rates = invgamma samplefreq=1000 nchains=4 stoprule=YES stopval=0.01 burninfrac=0.25 temp=0.25

Thank you!

Answer 1

[Mensur Dlakic]

Other than annealing temperature (too high, in my opinion), there is nothing obviously wrong with your parameters. You have to realize that there is no set of parameters that works for all alignments. For example, here is a set of parameters that often works form me, but sometimes it does not.

lset rates=invgamma nst=6 ngammacat=4;
prset statefreqpr=fixed(empirical);
mcmcp nruns=2 ngen=1000000 printfreq=1000 samplefreq=100 starttree=random;
mcmcp relburnin=yes burninfrac=0.25 mcmcdiagn=yes diagnfreq=1000 stoprule=yes stopval=0.0005;
mcmcp nchains=4 nswaps=2 allchains=yes checkfreq=1000 savebrlens=yes temp=0.1;

You need to find best parameters for your alignment. There is a program for that - see here or ModelFinder in IQ-TREE. You can also try doing the permutations manually. For example, you do the run with options listed above. Next time change rates=invgamma to rates=gamma and so forth. Beware that it typically takes much longer to do it manually as opposed to automatic selection.

By the way, I would try temp from one of the following values [0.05, 0.075, 0.1, 0.125] as 0.25 is probably too much heating.

[buhbs]

Thank you so much, Mensur Dlakic. I will try lowering the temp and using the model finder. I appreciate your insight!