Various orthology/homology detection methods under study

aAlternative orthology detection strategies (including phylogeny, distance or BLASTP-based), or homology detection methods.bParameters analyzed using the LCA benchmarking framework to assess their effect on orthology detection performance (Figure 4).cThe fraction of positively predicted protein pairs (using default parameter settings) within the entire sampling dataset of 567,255 cross-species homologous protein pairs (defined by Pfam domains).dThe average fraction of positively predicted protein pairs (using default parameter settings) from 100 sampling replicates (of the average total of 1590.15 pairs).