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

Next, a peptide file was generated using a custom scrit that extracts the longest putative transcript from the gene annotation GTF file. This peptide file was inserted into the genome assembly directory and used by gimme motifs2factors.

Finally, gimme motifs2factors was executed using this command:

gimme motif2factors \
--new-reference /path/to/Smed.fa \
--ortholog-references \
GRCz11 GRCg6a UCB_Xtro_10.0 BraLan2 oryLat2 ARS-UCD1.2 phaCin_unsw_v4.1 rCheMyd1.pri \
Mlig_3_7 El_Paco BDGP6.32 Hydra_RP_1.0 WBcel235 KH ASM20922v1 \
--genomes_dir /path/to/genomes \
--outdir /path/to/output_folder \
--tmpdir /path/to/output_folder/orthofinder_output \
--threads 48 \
--keep-intermediate