End of Tree file error

[Jackson Caudle]

Hello all, 

I am trying to run a selection analysis using codeml in PAML. I have gotten it to run, but it seems to run for about an hour then when conducting the ancestral reconstruction will stop and I get the end of tree file error. 

I am getting an output document but I am unsure if this error is ending the analysis short or if the error is supposed to happen. 

Any help would be greatly appreciated thank you. 

[Sandra AC]

Hi there,

Thanks for your message! 

Have you checked that you have included the PHYLIP header in your tree file? In addition, you will need to remove the branch lengths as specified in the Data formatting section in the PAML Wiki. By fixing the format in your tree file, you should get rid of that error message -- if the format is not followed but everything else in the output file looks fine, then the error message can be ignored.

Hope this has fixed the issue. Should you need anything else, please do not hesitate to reach out here!

All the best,
Sandy

P.S.: If that is your first attempt trying to use CODEML to detect positive selection, I also suggest you read our "Beginner's guide on the use of PAML to detect positive selection" (Álvarez-Carretero et al., 2023). The analyses detailed in the protocol can be reproduced if you follow the step-by-step tutorial in our GitHub repository "positive-selection" -- you have template scripts and the input/output files described in the protocol :)