Hi all. I am trying to construct a Bayesian analysis and phylogenetic tree using MrBayes with a set of 85 sequences with an alignment of 900 bp. 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!
Convergence in many cases reach in infinite time, of course depending on your hardware specifics. So, either you can change the parameters and try again or just quit analysis after X iterations and mention the specific parameters in your publication.
Further, no one can say which parameter to change for convergence. It is very specific to the data you are analysing.
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