codeml analysis for multiple alignments

Question

[sbissi102]

Hello Everyone,

I'd want to do a codeml analysis on many OG files created by orthofinder (including tree files). . I used "muscle" to construct the protein alignments, then "pal2nal" to convert all of the transcript into codon alignments. I was wondering if I should write several Codeml control files for each OG (over 1400) or if Codeml could be executed with a single ".ctl" file.!?

Suggestions appreciated. Thanks

Answer 1

[shelkmike]

When I had such a task, I wrote a script that automatically made a lot of .ctl files, one file for each orthogroup, and then run Codeml with them.

[sbissi102]

Thank you, In fact, I can't seem to locate the appropriate script.

Answer 2

[Roberto]

They explain something of the sort in this tutorial https://bioinformaticsworkbook.org/dataAnalysis/ComparativeGenomics/Finding_Positive_Selection_With_Codeml.html#gsc.tab=0

However, there's been an explosion of tools to automate paml and similar eg. https://pubmed.ncbi.nlm.nih.gov/31888452/

[sbissi102]

Thank you, Roberto. I attempted to follow the first instruction, but I am unable to generate the.clt files for the various orthogroups! In truth, I am unable to write the script.