Codeml does not produce mlc files, it combines with the output

[kdbchau]

trafficstars

Hello!

Codeml does not produce separate mlc files anymore, the data are merged with the general output file defined in codeml.ctl. I was wondering if I could see an actual mlc output file so I could make my own that I can then use with ggtree? I need to plot the dN/dS values along branches and read.codeml does not seem to work with my rst file or general output files. Thanks!

[paula-torres]

Hi, did you solve this issue? I have the same problem

[kdbchau]

Nope. Never solved and never got help with it so I just don't use it.