BUSCO_v5.2.2_eukaryota_odb10.EukProt_v03.2021_11_22.txt : results of running BUSCO v5.2.2 with the eukaryota_odb10 database on all protein files from EukProt.

The_Comparative_Set_196_species.EukProt_v03.2021_11_22.txt : list of protein files included in The Comparative Set (TCS).

OrthoFinder2 orthogroups inferred from The Comparative Set (on FigShare, contributed by Chung Hyun Cho) : the construction of orthologous gene clusters, referred to as orthogroups, was carried out for The Comparative Set (TCS), which encompasses a total of 196 eukaryotic species. The clustering of genes in a non-biased manner was performed using Orthofinder v2.5.2, wherein each gene was compared to a comprehensive proteome dataset consisting of over five million proteins. Following the experimentation with various parameters, the DIAMOND algorithm was selected for conducting homology searches using the '-S diamond_ultra_sens' option.

Pfam v34.0 protein domain annotations (on FigShare, contributed by Alex Gàlvez-Morante): Pfam domains predicted on all EukProt v3 datasets (one output file per dataset). Domains were predicted with InterProScan version 5.56 and InterPro version 89.0 (which includes the Pfam database version 34.0; note that this is no longer the most recent version of Pfam), with default parameter values.