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