Orthofinder giving really unexpected results

[kkrizanovic]

Hello, I've been running Orthofinder to compare a newly assembled genome (proteome) to several closely related species and one not so closely related. I've downloaded proteins for other species from NCBI. I've gotten some strange results.

1. I get no Single copy orthologues. My guess is that this is due to many copies of most proteins in NCBI datasets. Do you have any advice on how to filter my data and remove duplicate proteins/genes? I've tried downloading protein sets from ensembl, but it only has data for 4 out of 10 species that I would like.
2. When I look at phylogenetic tree (folder Species_Tree) it seems incorrect. The outgroup species (one biologically not closely related) is placed as very closely related to others.

Do you have any advice on how to proceed in obtaining a better phylogenetic tree for my data?

[shiyi-pan]

Hi,kkrizanovic, I met the some problem, Could you fix it?