Difference between revisions of "Using Mr Bayes to For Phlyogenetic Analysis"
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Revision as of 19:22, 9 September 2009
Software
- Mr Bayes for detailed instructions see the manual
- Sequence Alignment Software (CLUSTALX or MUSCLE)
Analysis
- Generate sequence alignment and save as a nexus formatted file.
- Move file to Mr Bayes directory
- May need to edit the file to remove the line defining symbols.
- Type execute filename.exe with your filename specified
- Type lset nst=6 rates=invgamma
- Type mcmc ngen=10000 samplefreq=10. If the average standard deviation is below 0.01 then type no to continue. Else type yes until it reaches this threshold.
- Type sump burnin=250, where 250 is 25% of your generations. For example if you ran 10 000 generations (sampled 1000 generations, you would use 250). Check that the potential scale reduction factor (PSRF) is close to 1.0 for all samples. If it is not run some more generations
- Type sump burnin=250, where 250 is the same parameter as above. This will output both a cladogram and a tree file
- Transfer all files into another directory for saving.
