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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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Running IQTREE or RAxML separately #810

Open m3hdad opened 1 year ago

m3hdad commented 1 year ago

Hi Orthofinders,

This is not an issue but seeking recommendation.

I was wondering if anyone has a suggestion how to run gene tree inference by IQTREE/ RAxML separately. I've divided the workflow in three parts:

  1. orthofinder with -oa option
  2. slurm array jobs for iqtree/raxml
  3. orthofinder with -ft

However I fail to submit part 3 and resume orthofinder with -ft option as I cannot figure out how orthofinder reads gene-tree inferred by iqtree/raxml. It stops with the error indicating that species tree does not exist. My understanding was that -ft resumes from gene tree and not species tree. But apparently I did not understand the workflow.

In addition, for iqtree/raxml I only feed in single-copy MSA in p% of species which are listed under Species_Tree/Orthogroups_for_concatenated_alignment.txt when -oa is used.

Thanks in advance for any suggestions.

davidemms commented 1 year ago

Hi

The rooted species tree is required in order to be able to root the gene trees and thus infer orthologs. It sounds like what you have done is correct, but you will need to infer the rooted species tree too in order to carry out part 3 of your analysis.

Best wishes David

m3hdad commented 1 year ago

Thanks for your feedback. I'll take this into consideration on my next attempt.

Regards,