PhyloBayes trace outfile

Question

[Yosi]

Hi there,

I'm new here and in the field of MCMCMC. I screened already all questions but couldn't find an answer to my problem.

So, I'm working with PhyloBayes and I'm wondering what the different columns in the *.trace outfile mean. Some points are clear, some more or less, but most of them depict a mystery for me. Maybe someone of you is more fit in this topic? Many thanks for your help!

• #cycle: that's clear ;)
• #treegen
• time
• loglik: that's also clear :) (log likelihood)
• length
• sigma: standard deviation of a Gaussian distribution?
• mu: mean of a Gaussian distribution?
• meanrates
• scale
• alpha
• nocc
• stat
• statalpha
• rrent
• meanrr
• kappa: ratio between transitions and transversions
• allocent