Hi there,
It seems that you had double brackets to specify a clade (i.e., same clade was repeated twice with the opening/closing parentheses). The issue was here:
If you use an IDE such as Visual Studio Code or a text editor such as Notepad++ or Sublime (there are many more, just naming some!), it would be easier for you (and for other users who may encounter this problem) to identify whereabouts there are additional parentheses in your Newick-formatted tree :)
In addition, please note that the PAML-X GUI has not been maintained for years, and hence its usage is not recommended. Instead, all PAML programs should be executed via the terminal. I am not entirely sure what kind of analysis you want to run with CODEML as there are many options in the control file that perhaps you do not even need to have there (not sure how you generated the control file nor the analysis you are running, so just guessing!). If you want to run CODEML to test for positive selection, however, then I suggest you read our
latest protocol "Beginner's guide on the use of PAML to detect positive selection" (Álvarez-Carretero et al., 2023), where we explain in detail the various steps to follow to run such tests with CODEML. You should read this protocol alongside
our `positive-selection` GitHub repository -- they are supposed to be read together as theory+practical! You can find various template control files that you can use to run your analyses depending on which model you want to run (e.g.,
homogenous model,
site models,
branch models,
branch-site models) -- just follow the instructions in the `README.md` files :)
Hope these suggestions help with your analyses!
All the best,
S.