Hi Phylobabble community,
I’m wondering what precisely is alpha, statalpha, rrment, statent and Nmode parameters from the trace file of phylobayes ? I read carefully the phylobayes manual v4.4 and mpi v1.7, but I have always some trouble to understand exactly what I’m doing. I suspect “Nmode” to be linked to “K”, the number of classes when using a cat model according Lartillot and Philippe, 2004 ?
Where can I find documents to understand who is who, which one is connected to the substitution model (or where can I found estimates to check them over iterations ?) ?
I will really appreciate if you can help me a bit