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Using Mr Bayes to For Phlyogenetic Analysis

49 bytes added, 14:42, 13 September 2009
changed instructions for burnin
#Type '''lset nst=6 rates=invgamma'''. This is for nucleotide, for protein use '''prset aamodelpr=mixed'''
#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 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
#Type '''sumt 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.
#View tree using TreeView