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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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is it possible to specify a tree for orthofinder? #893

Open AlexGalvez opened 5 months ago

AlexGalvez commented 5 months ago

I have the correct species tree for an analysis and I would want orthofinder to use it to detect orthologs; it possible to specify a tree for orthofinder?

lauriebelch commented 5 months ago

Hi Alex,

Yes it is. The easiest way to do this is to run OrthoFinder first, and then reanalyse with your tree.

You can do this using the option

-ft PREVIOUS_RESULTS_DIR -s SPECIES_TREE_FILE

This should be quite quick, as it just runs the final steps

Thanks,

Laurie