Benchmarking comparison of different orthology inference algorithms. The reference set used in the benchmark of Hulsen et al.  is taken as a gold standard to compute the number of true positives (TP), false positives (FP) and false negatives (FN) yielded by each method. For each method the sensitivity (S = TP/(TP+FN)) and the positive predictive value (P = TP/(TP + FP)) are computed. Methods described in  are indicated as BBH (Best reciprocal hits), MCL (OrthoMCL), ZIH (Z-score 1-hundred.), INP (Inparanoid), PGT (phylogeny-based algorithm used in ), KOG (Clusters of eukaryotic orthologous goups). 'Phylome' represents the results of our pipeline and algorithm, and Ensbl the orthology relationships predicted by Ensembl database.