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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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Percentage of single copy gene trees in agreement with species tree #599

Open palomo11 opened 3 years ago

palomo11 commented 3 years ago

Hi,

I have run OrthoFinder with 4 genomes belonging to the same species and I would like to know how many of the single copy gene trees have the same topology as the species tree. Is something that can be found with OrthoFinder output?

Thanks in advance!

davidemms commented 3 years ago

Hi

No, this isn't a statistic calculated by OrthoFinder. I think you could do this by writing a script using the ETE python library to calculate the Robinson-Foulds distance between the trees if you replaced the the gene names in the single-copy gene trees with the species tree.

All the best David

palomo11 commented 3 years ago

Hi David,

Thank you very much for the suggestion. I will try that.