I am using the BSG model, and I don't understand where are the results for the values of dn/ds for each branch. Are they supposed to be in the json file (which is a bit complicated to follow) or in the std.out file?
Also, in the documattion it says "A heuristic to avoid LRT statistics overestimation, which often causes false positives in PAML. Also corrects for LRT underestimation. Use godon test to enable."
To implement this I need to run another code or is it the default when I run all models? If not how to run it?
godon test BSG --m0-tree --procs 60 --json=dunce.json --all-branches --ncat-codon-rate 4 seq.fasta tree.nwk > res.std.out
Thanks. godon is a great software!
