Hi Nathanael,
Input tree files should not have branch lengths/bootstrap values in order to avoid possible "clashes" with the labels that users can specify to enable specific features available in PAML programs such as CODEML or MCMCtree.
When using CODEML to test for positive selection, if there are no clashes between "PAML labels" specified by users and "branch lengths/bootstrap values/other labels" present in the Newick tree, CODEML may be able to ignore them and run without errors (i.e., they will not impact the analysis). Nevertheless, this is not always the case, and that is the reason for asking users to remove branch lengths and other labels that may interfere with other PAML labels and stop CODEML from running. For details on
template control files you can use to run CODEML under various scenarios, you can also check
the GitHub repository we published last year.
If you are using CODEML for ancestral state reconstruction or other analyses, you may have to specify whether you want to keep the branch lengths as "starting values" -- note that this is a different type of analysis from the one Janani was referring to. In that case, branch lengths may be required if users want to use them as starting values. You can find more details about other analyses you can run with CODEML and how to enable them in
the PAML documentation.
Hope this helps and clarifies your doubts :)
S.