Comparing the number of true positives and false positives for six different methods on three datasets using only one-to-one pairs. Plot of number of true positives vs number of false positives in the output of BBH-LS (α = 0.50, β = 0.00), BBH, MSOAR2, InParanoid, OMA, and Ensembl Compara for the human-mouse, human-rat, and mouse-rat dataset. Only the one-to-one pairs were used in this analysis. For InParanoid, each many-to-many pair is converted to a one-to-one pair by extracting the seed ortholog pair. For OMA and Ensembl, the many-to-many pairs are discarded.