is it possible to specify a tree for orthofinder?

[AlexGalvez]

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]

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