Simulation options for bppseqgen
Hi all,
I noticed that, in the file bppsuite.ml, there are some strings for the bppseqgen config file which don't appear in the bpp manual (e.g. "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_1))"
). I assume these enable simulation of coding alignments under a given amino acid frequency vector. However, they don't appear to be available in the current bppsuite release. Are these models that are currently implemented in bppseqgen which I have missed, or were they implemented just for the paper?
Thanks in advance for your help,
Best,
Nathanael