1. Bayesian inference with MrBayes Molecular Phylogenetics – exercise

2. 1. MrBayes
1.1 Overview on MrBayes
Implements the Metropolis-Hastings-Green-algorithm.
Analyses can be started from the internal command line (just like in PAUP*).
The help command displays a list of available commands.
help <command> displays help to a certain commend.
More information under
Command reference under

3. 1.2 Important commands to start an analysis
1. MrBayes
1.2 Important commands to start an analysis
execute <alignmentFile>: Reads alignment data from a file (e.g. Nexus).
lset: Can be used to set the model parameters (e.g. nst=6 rates=invgamma sets the GTR+I+G model)
mcmc: Starts an MCMC analysis with the loaded alignment.
ngen: The number of generations for the chain to run.
samplefreq: The frequency of generations when a tree shall be written to the log file
printfreq: The frequency to print information on the current run to the command line.
diagnfreq: The frequency to analize the current process (e.g. the measure of the similarity of the current tree samples).
savebrlens: Specify yes here, if branch lengths shall be saved.
nchains: Specifies the number of parallel chains (default is 4).

4. 1.3 Important commands to finish an analysis
1. MrBayes
1.3 Important commands to finish an analysis
plot: Plots the deveopment of an estimated parameter over time (The parameter to be displayed can be selected.)
sump: Summarize samples of model parameters (section in manual)
sumt: Summarize the tree samples

5. 1. MrBayes
1.4 Running an analysis
During an analysis the current ln(linkelihood) of all chains are printed out.
run 1
diagnosis output
run 2
heated chains
cold chain

6. 1.5 Continuing the analysis
1. MrBayes
1.5 Continuing the analysis
After the specified number of generations has been reached, you are asked, if you want to continue the chain.
The average deviation of split frequencies should be below 0.01 in order to stop the chain

7. 1. MrBayes
1.6 Output files
MrBayes produces several output files in your working directory
run1.p and run2.p contain the development of the model parameters during the chain
Can be opened e.g. in Excel
run1.t and run2.t contain the tree samples collected during the chain
In NEXUS format
Can be opened with TreeGraph 2 (or other tree editors)
After calling sumt, the result tree is contained in the con-file.