Round 1 phylogenetic trees

[santule]

Hello @seanrjohnson ,

Thank you for the amazing study and paper. I am looking for phylogenetic trees used in round 1 of the study. I could not find them in Zenodo. What is the best location to get them ?

Thanks.

[seanrjohnson]

Do you mean trees of the experimentally tested sequences or the training (wild-type) sequences?

I think we did not generate trees of the tested sequences. For training sequences, we only generate trees for the purpose of running ASR. I don't know if we have any of those trees. They are not Zenodo. If that's what you want, I can ask the other authors if they have them. Would you like me to ask?

We do supply MSAs of training sequences. These are the MSAs used to generate the ASRs. They are in Zenodo, in sequences.zip / train_test_splits / *-msa.fasta

To convert to trees, you would just need to run fasttree, I think with default settings.