Public Results 2022




This benchmark samples orthologs following a comb species tree from eukaryota species, infers gene trees from them and compare them with the expected species tree. Details on this benchmark are available in Altenhoff and Dessimoz, 2019 Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PLoS Computational Biology, 5(1): e1000262.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project Number of predicted pairwise ortholog relationsNumber of completed tree samples (out of 50k trials) Avg Robinson-Foulds distance (genetree, exp. speciestree)Fraction of incorrect trees
BBH_(SW_alignments) 2462889912 +- 141 0.0464 +- 0.00290.1007 +- 0.0059
Domainoid+ 38108713464 +- 134 0.0452 +- 0.00240.1024 +- 0.0051
Hieranoid_2 29073010296 +- 141 0.0340 +- 0.00250.0736 +- 0.0050
OMA_Groups 2094437745 +- 136 0.0351 +- 0.00300.0727 +- 0.0058
OMA_HOGs 3234007395 +- 135 0.0407 +- 0.00320.0863 +- 0.0064
OMA_Pairs 33188510339 +- 141 0.0396 +- 0.00270.0851 +- 0.0054

This benchmark samples orthologs following a comb species tree from fungi species, infers gene trees from them and compare them with the expected species tree. Details on this benchmark are available in Altenhoff and Dessimoz, 2019 Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PLoS Computational Biology, 5(1): e1000262.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project Number of predicted pairwise ortholog relationsNumber of completed tree samples (out of 50k trials) Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
BBH_(SW_alignments) 996619399 +- 166 0.6602 +- 0.00960.3247 +- 0.0055
Domainoid+ 1190969982 +- 170 0.6629 +- 0.00930.3354 +- 0.0055
Hieranoid_2 1010648627 +- 161 0.633 +- 0.0100.3109 +- 0.0058
OMA_Groups 605195115 +- 131 0.576 +- 0.0140.2849 +- 0.0076
OMA_HOGs 803565716 +- 137 0.603 +- 0.0130.2969 +- 0.0072
OMA_Pairs 855526685 +- 146 0.616 +- 0.0120.3043 +- 0.0066

This benchmark samples orthologs following a comb species tree from bacteria species, infers gene trees from them and compare them with the expected species tree. Details on this benchmark are available in Altenhoff and Dessimoz, 2019 Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PLoS Computational Biology, 5(1): e1000262.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project Number of completed tree samples (out of 50k trials)Number of predicted pairwise ortholog relations Avg Robinson-Foulds distance (genetree, exp. speciestree)Fraction of incorrect trees
BBH_(SW_alignments) 985 +- 5814026 0.569 +- 0.0180.914 +- 0.018
Domainoid+ 1220 +- 6420812 0.593 +- 0.0160.933 +- 0.014
Hieranoid_2 1028 +- 6016730 0.571 +- 0.0180.911 +- 0.017
OMA_Groups 577 +- 4610717 0.516 +- 0.0240.875 +- 0.027
OMA_HOGs 1126 +- 6230557 0.584 +- 0.0180.909 +- 0.017
OMA_Pairs 871 +- 5520025 0.551 +- 0.0200.898 +- 0.020

This benchmark samples orthologs from randomly sub-sampled species trees from the luca clade, infers a gene tree from each sampled group and compares them with the expected species tree. Details on this benchmark are available in Altenhoff A et al., 2020 The Quest for Orthologs benchmark service and consensus calls in 2020. Nucl. Acids Res., 48:W1, W538–W545.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project Number of predicted pairwise ortholog relationsNumber of completed tree samples (out of 50k trials) Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
BBH_(SW_alignments) 51546321209 +- 67 0.864 +- 0.0190.264 +- 0.010
Domainoid+ 123754941921 +- 84 0.863 +- 0.0150.2703 +- 0.0082
Hieranoid_2 8111432832 +- 56 0.843 +- 0.0250.256 +- 0.012
OMA_Groups 3192599202 +- 28 0.876 +- 0.0460.248 +- 0.023
OMA_HOGs 50934088438 +- 41 0.847 +- 0.0340.253 +- 0.017
OMA_Pairs 7482099550 +- 46 0.860 +- 0.0290.255 +- 0.014

This benchmark samples orthologs from randomly sub-sampled species trees from the eukaryota clade, infers a gene tree from each sampled group and compares them with the expected species tree. Details on this benchmark are available in Altenhoff A et al., 2020 The Quest for Orthologs benchmark service and consensus calls in 2020. Nucl. Acids Res., 48:W1, W538–W545.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project Number of completed tree samples (out of 50k trials)Number of predicted pairwise ortholog relations Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
BBH_(SW_alignments) 3646 +- 1144251345 0.814 +- 0.0140.2322 +- 0.0062
Domainoid+ 5162 +- 13310196468 0.819 +- 0.0140.2368 +- 0.0063
Hieranoid_2 3643 +- 1147004479 0.800 +- 0.0140.2220 +- 0.0061
OMA_Groups 1063 +- 632772338 0.766 +- 0.0260.205 +- 0.010
OMA_HOGs 2981 +- 10450074914 0.820 +- 0.0140.2367 +- 0.0062
OMA_Pairs 2369 +- 936593688 0.802 +- 0.0160.2256 +- 0.0070

This benchmark samples orthologs from randomly sub-sampled species trees from the vertebrata clade, infers a gene tree from each sampled group and compares them with the expected species tree. Details on this benchmark are available in Altenhoff A et al., 2020 The Quest for Orthologs benchmark service and consensus calls in 2020. Nucl. Acids Res., 48:W1, W538–W545.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project Number of predicted pairwise ortholog relationsNumber of completed tree samples (out of 50k trials) Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
BBH_(SW_alignments) 99440322467 +- 218 0.912 +- 0.0100.2409 +- 0.0058
Domainoid+ 153098626048 +- 219 0.915 +- 0.0100.2443 +- 0.0059
Hieranoid_2 119469619828 +- 214 0.913 +- 0.0100.2332 +- 0.0054
OMA_Groups 89445714826 +- 200 0.899 +- 0.0110.2278 +- 0.0054
OMA_HOGs 160462218472 +- 212 0.906 +- 0.0100.2315 +- 0.0054
OMA_Pairs 160846119658 +- 214 0.912 +- 0.0100.2355 +- 0.0058

This benchmark samples orthologs from randomly sub-sampled species trees from the fungi clade, infers a gene tree from each sampled group and compares them with the expected species tree. Details on this benchmark are available in Altenhoff A et al., 2020 The Quest for Orthologs benchmark service and consensus calls in 2020. Nucl. Acids Res., 48:W1, W538–W545.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project Number of predicted pairwise ortholog relationsNumber of completed tree samples (out of 50k trials) Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
BBH_(SW_alignments) 23138711268 +- 183 0.680 +- 0.0170.2697 +- 0.0086
Domainoid+ 28241612319 +- 189 0.685 +- 0.0170.2752 +- 0.0087
Hieranoid_2 23702810157 +- 176 0.668 +- 0.0170.2619 +- 0.0085
OMA_Groups 1398863941 +- 118 0.616 +- 0.0170.2271 +- 0.0079
OMA_HOGs 1928176556 +- 148 0.630 +- 0.0170.2401 +- 0.0082
OMA_Pairs 2020166581 +- 148 0.647 +- 0.0170.2467 +- 0.0083

This benchmark compares the predicted orthologs with the orthologs from a set of manually curated reference gene trees. Details on this benchmark are available in Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz, 2011 Conceptual Framework and Pilot Study to Benchmark Phylogenomic Databases Based on Reference Gene Trees. Briefings in Bioinformatics, 12:5 (pp. 474-484).

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project True positive rate Positive predictive value rate
BBH_(SW_alignments) 0.570 +- 0.037 0.932 +- 0.036
Domainoid+ 0.759 +- 0.035 0.932 +- 0.030
Hieranoid_2 0.726 +- 0.036 0.950 +- 0.030
OMA_Groups 0.496 +- 0.038 0.940 +- 0.036
OMA_HOGs 0.696 +- 0.035 0.924 +- 0.030
OMA_Pairs 0.677 +- 0.035 0.929 +- 0.031

This benchmark compares the predicted orthologs with the orthologs implied from the reconciled gene trees from tree fam. Details on this benchmark are available in Heng Li et. al, 2006 TreeFam: a curated database of phylogenetic trees of animal gene families. Nucl. Acids Res., 34(suppl 1): D572-D580.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project True positive rate Positive predictive value rate
BBH_(SW_alignments) 0.4828 +- 0.0066 0.9560 +- 0.0038
Domainoid+ 0.6715 +- 0.0062 0.9231 +- 0.0041
Hieranoid_2 0.6206 +- 0.0064 0.9300 +- 0.0041
OMA_Groups 0.3828 +- 0.0064 0.9535 +- 0.0044
OMA_HOGs 0.5799 +- 0.0065 0.9231 +- 0.0044
OMA_Pairs 0.5650 +- 0.0066 0.9199 +- 0.0046

This benchmark compares the predicted orthologs with some manually curated and asserted orthologs from the VGNC consortium. Details on this benchmark are available in Tweedie S et al., 2021 Genenames.org: the HGNC and VGNC resources in 2021. Nucl. Acids Res., 49:D1, D939-D946.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project True positive rate Positive predictive value rate
BBH_(SW_alignments) 0.9790 +- 0.0020 0.99974 +- 0.00023
Domainoid+ 0.9856 +- 0.0017 0.99535 +- 0.00096
Hieranoid_2 0.9532 +- 0.0030 0.99780 +- 0.00067
OMA_Groups 0.9447 +- 0.0032 0.99919 +- 0.00041
OMA_HOGs 0.9709 +- 0.0024 0.9790 +- 0.0020
OMA_Pairs 0.9716 +- 0.0023 0.9801 +- 0.0020

This benchmark computes how well the gene ontology annotations are conserved among the predicted orthologs. Details on this benchmark are available in Altenhoff and Dessimoz, 2019 Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PLoS Computational Biology, 5(1): e1000262.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project Number of predicted pairwise ortholog relations Avg Schlicker similarity
BBH_(SW_alignments) 88910 0.5115 +- 0.0015
Domainoid+ 169998 0.4851 +- 0.0011
Hieranoid_2 126270 0.4938 +- 0.0013
OMA_Groups 62952 0.5167 +- 0.0018
OMA_HOGs 362533 0.41686 +- 0.00072
OMA_Pairs 110960 0.4964 +- 0.0014

This benchmark computes how well the Enzyme Commission numbers are conserved among the predicted orthologs. Details on this benchmark are available in Altenhoff and Dessimoz, 2019 Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PLoS Computational Biology, 5(1): e1000262.

This is an interactive plot of the results. You can enable/disable methods by clicking on the label in the legend, or hover over the data points to get extra information. The measures we use for precession and recall are explained in the documentation section.

Project Number of predicted pairwise ortholog relations Avg Schlicker similarity
BBH_(SW_alignments) 148769 0.95149 +- 0.00076
Domainoid+ 220046 0.91590 +- 0.00082
Hieranoid_2 169100 0.94776 +- 0.00073
OMA_Groups 99657 0.97144 +- 0.00072
OMA_HOGs 308308 0.82920 +- 0.00092
OMA_Pairs 156000 0.95220 +- 0.00073