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Mr Bayes quick start guide 1. Type "help" on the MrBayes prompt to see the list of the commands
 

Summary: Mr Bayes quick start guide
1. Type "help" on the MrBayes prompt to see the list of the commands:
MrBayes> help
Or type "help " :
MrBayes> help lset
MrBayes> help mcmc
MrBayes> help sumt
2. Read in a data file in nexus format:
MrBayes> execute primates.nex
3. Specify the evolutionary model (eg, GTR+G+I):
MrBayes> lset nst=6 rates=invgamma
4. Run the analysis (specify how long the chains should be):
MrBayes> mcmc ngen=10000 samplefreq=10
Watch the standard deviation of split frequencies (ideally it should go below 0.01)
5. Summarize the parameter values discarding the beginning of the run (~25%):
MrBayes> sump burnin=250
6. Summarize the trees discarding the beginning of the run (~25%):
MrBayes> sumt burnin=250
7. The trees may be viewed using TreeView, MacClade, Mesquite, ATV-Forester
8. Happy MrBaeysing!

  

Source: Anisimova, Maria - Institute of Scientific Computing, Eidgenössische Technische Hochschule Zürich (ETHZ)

 

Collections: Biology and Medicine