Orthologues were determined using Gimmemotifs, Orthofinder and GFFread. A new conda environment was created containing the packages listed below. 

Conda environment:
 - gimmemotifs-minimal 0.18.0
 - orthofinder 2.5.5
 - gffread 0.12.7

Finally, gimme motifs2factors was executed using this command:

gimme motif2factors \
--new-reference /path/to/Smed.fa \
--ortholog-references \
GRCz11 GRCg6a UCB_Xtro_10.0 BraLan3 ASM223467v1 ARS-UCD1.2 phaCin_unsw_v4.1 rCheMyd1.pri.v2 \
Mlig_3_7 El_Paco_v._4 BDGP6.46 Hydra_105_v3 WBcel235 KH ASM20922v1 \
--genomes_dir /path/to/genomes \
--outdir /path/to/output_folder \
--tmpdir /path/to/output_folder/orthofinder_output \
--threads 48 \
--keep-intermediate