This routine reformats the orthogroups in the N0.tsv file into a tab-delimited row format with only protein names.
For example, if you ran OrthoFinder in the At_Mus directory (containing the FASTAs), you'll get the following file:
At_Mus/OrthoFinder/Results_Feb01/Phylogenetic_Hierarchical_Orthogroups/N0.tsv
In this case, run reformat-pho as follows:
$ cd At_Mus/OrthoFinder/Results_Feb01/
$ ../../../reformat-pho > pho.tsv
This will create a file pho.tsv which contains the orthogroup identifiers, e.g.
HOG OG Gene Tree Parent Clade Arabidopsis_thaliana.TAIR10.pep.all Mus_musculus-Cilia_proteome
N0.HOG0000000 OG0000000 n0 AT5G09950.2 AT5G09950.3 AT5G09950.1 AT4G33170.1 AT1G16480.1 ...
Note that the top lines of this file are very long because they contain large At orthogroups. Groups that contain Mus genes are further down in the file.