If the branch lenghth in species tree are necessary in my analysis using hyphy?

[Neo-xbx-00]

Dear hyphy users and developers,
I found it really convenient for using this tool to identity selections among species. Here, I face an issue and hope you to help me out. Now, I have only three species:
(1) I use Orthofinder software to get gene orthologs among these species, which include orthologs containing the single-copy genes in these species.
(2) Then, I choose the above single-copy orthologs and conduct analysis using hyphy. However, as I only have three species, I can not have branch length in my species tree, which looks like this, all branch lenth have been set to 1:
((Emal:1,Erad:1):1,Lbre:1):1;
So, I wonder if the species tree lack branch length will have negative influence on hyphy analysis and models?
Best regards!
(From https://github.com/veg/hyphy/)