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Using Mr Bayes to For Phlyogenetic Analysis

Software

  • Mr Bayes for detailed instructions see the manual
  • Sequence Alignment Software (CLUSTALX or MUSCLE)

Analysis

  1. Generate sequence alignment and save as a nexus formatted file.
  2. Move file to Mr Bayes directory
  3. May need to edit the file to remove the line defining symbols.
  4. Type execute filename.exe with your filename specified
  5. Type lset nst=6 rates=invgamma. This is for nucleotide, for protein use prset aamodelpr=mixed
  6. 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.
  7. Type sump burnin=250, where 250 is 25% of your generations. For example if you ran 10 000 generations (sampled every tenth for 1000 generations sampled) 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
  8. Type sumt burnin=250, where 250 is the same parameter as above. This will output both a cladogram and a tree file
  9. Transfer all files into another directory for saving.
  10. View tree using TreeView
Last modified on 13 September 2009, at 14:42