Public Results 2018




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) Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
BBH 25396410438 +- 142 0.1038 +- 0.00590.0481 +- 0.0029
Broccoli_1.1 49248713975 +- 134 0.1365 +- 0.00570.0653 +- 0.0030
eggNOG 30922910514 +- 142 0.1145 +- 0.00610.0541 +- 0.0031
Ensembl_Compara 91946914771 +- 130 0.1489 +- 0.00570.0657 +- 0.0027
Hieranoid2 37005711268 +- 142 0.0783 +- 0.00500.0355 +- 0.0024
InParanoid 37297213265 +- 137 0.0754 +- 0.00450.0334 +- 0.0021
OMA_GETHOGs_2.0 9792109022 +- 141 0.0957 +- 0.00610.0440 +- 0.0030
OMA_Groups_2.0 2211557797 +- 137 0.0775 +- 0.00590.0383 +- 0.0031
OMA_Pairs_2.0 38808710485 +- 142 0.0865 +- 0.00540.0399 +- 0.0026
OrthoFinder_2_BLAST__DendroBLAST_ 44080614015 +- 134 0.1195 +- 0.00540.0533 +- 0.0026
OrthoFinder_2_BLAST__MSA 44883014362 +- 132 0.1371 +- 0.00560.0607 +- 0.0027
OrthoFinder_2_Defaults_DIAMOND__MSA 39750413366 +- 137 0.1126 +- 0.00540.0503 +- 0.0026
OrthoFinder_2_DIAMOND__MSA 42292013584 +- 136 0.1257 +- 0.00560.0564 +- 0.0027
OrthoInspector_3.0 35383212686 +- 139 0.0946 +- 0.00510.0423 +- 0.0024
OrthoMCL 79862711198 +- 142 0.3873 +- 0.00900.2612 +- 0.0068
PANTHER_14.1_all 50382114632 +- 131 0.1201 +- 0.00530.0538 +- 0.0025
PANTHER_14.1_LDO_only 2445507589 +- 136 0.0822 +- 0.00620.0375 +- 0.0030
Proteinortho_5.16b 2729547992 +- 138 0.2310 +- 0.00920.1426 +- 0.0063
Proteinortho_6.0.13 2604608193 +- 139 0.1695 +- 0.00810.0997 +- 0.0052
RSD 25074811637 +- 141 0.1501 +- 0.00650.0717 +- 0.0034
SonicParanoid_default 40199212406 +- 140 0.0825 +- 0.00480.0373 +- 0.0023
SonicParanoid_most 41566812914 +- 138 0.0858 +- 0.00480.0380 +- 0.0023
SonicParanoid_sensitive 41585012867 +- 138 0.0817 +- 0.00470.0362 +- 0.0022

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) Avg Robinson-Foulds distance (genetree, exp. speciestree)Fraction of incorrect trees
BBH 1018239703 +- 168 0.3314 +- 0.00560.6567 +- 0.0094
Broccoli_1.1 13265910601 +- 173 0.3508 +- 0.00550.6771 +- 0.0089
eggNOG 1123929509 +- 167 0.3286 +- 0.00560.6595 +- 0.0095
Ensembl_Compara 14770610346 +- 172 0.3668 +- 0.00580.6856 +- 0.0089
Hieranoid2 1068449045 +- 164 0.3178 +- 0.00570.6448 +- 0.0099
InParanoid 1069499054 +- 164 0.3177 +- 0.00570.6427 +- 0.0099
OMA_GETHOGs_2.0 868405459 +- 135 0.3026 +- 0.00750.607 +- 0.013
OMA_Groups_2.0 606425153 +- 131 0.2893 +- 0.00760.584 +- 0.013
OMA_Pairs_2.0 855616683 +- 146 0.3046 +- 0.00670.615 +- 0.012
OrthoFinder_2_BLAST__DendroBLAST_ 14399711342 +- 177 0.3463 +- 0.00530.6770 +- 0.0086
OrthoFinder_2_BLAST__MSA 14360611291 +- 177 0.3457 +- 0.00530.6733 +- 0.0087
OrthoFinder_2_Defaults_DIAMOND__MSA 13748210912 +- 175 0.3383 +- 0.00530.6666 +- 0.0088
OrthoFinder_2_DIAMOND__MSA 14062610932 +- 175 0.3432 +- 0.00530.6724 +- 0.0088
OrthoInspector_3.0 12262810373 +- 172 0.3366 +- 0.00540.6679 +- 0.0091
OrthoMCL 14697310902 +- 175 0.4079 +- 0.00600.7207 +- 0.0084
PANTHER_14.1_all 15467711603 +- 178 0.3776 +- 0.00550.6985 +- 0.0084
PANTHER_14.1_LDO_only 969989440 +- 167 0.3332 +- 0.00570.6637 +- 0.0095
Proteinortho_5.16b 732095992 +- 140 0.3283 +- 0.00750.635 +- 0.012
Proteinortho_6.0.13 751686188 +- 142 0.2997 +- 0.00700.601 +- 0.012
RSD 983749180 +- 165 0.3349 +- 0.00590.6563 +- 0.0097
SonicParanoid_default 1035908647 +- 161 0.3190 +- 0.00580.647 +- 0.010
SonicParanoid_most 1156139879 +- 169 0.3317 +- 0.00550.6626 +- 0.0093
SonicParanoid_sensitive 1149599629 +- 168 0.3253 +- 0.00550.6552 +- 0.0095

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 1064 +- 6015114 0.576 +- 0.0180.914 +- 0.017
Broccoli_1.1 1079 +- 6119862 0.576 +- 0.0180.913 +- 0.017
eggNOG 719 +- 5113761 0.536 +- 0.0210.903 +- 0.022
Ensembl_Compara 1127 +- 6225508 0.590 +- 0.0180.912 +- 0.017
Hieranoid2 1029 +- 6017149 0.572 +- 0.0180.907 +- 0.018
InParanoid 1070 +- 6118065 0.575 +- 0.0170.918 +- 0.016
OMA_GETHOGs_2.0 1414 +- 6848871 0.624 +- 0.0160.921 +- 0.014
OMA_Groups_2.0 575 +- 4610742 0.511 +- 0.0240.875 +- 0.027
OMA_Pairs_2.0 868 +- 5520002 0.553 +- 0.0200.900 +- 0.020
OrthoFinder_2_BLAST__DendroBLAST_ 1105 +- 6122093 0.586 +- 0.0170.924 +- 0.016
OrthoFinder_2_BLAST__MSA 1088 +- 6121426 0.591 +- 0.0170.930 +- 0.015
OrthoFinder_2_Defaults_DIAMOND__MSA 1047 +- 6020404 0.577 +- 0.0180.914 +- 0.017
OrthoFinder_2_DIAMOND__MSA 1047 +- 6020015 0.576 +- 0.0180.913 +- 0.017
OrthoInspector_3.0 1177 +- 6319779 0.594 +- 0.0170.928 +- 0.015
OrthoMCL 1614 +- 7227878 0.659 +- 0.0150.944 +- 0.011
PANTHER_14.1_all 1160 +- 6327609 0.618 +- 0.0170.930 +- 0.015
PANTHER_14.1_LDO_only 931 +- 5712525 0.568 +- 0.0190.915 +- 0.018
Proteinortho_5.16b 825 +- 5412964 0.561 +- 0.0200.908 +- 0.020
Proteinortho_6.0.13 757 +- 5212182 0.542 +- 0.0210.906 +- 0.021
RSD 1031 +- 6015373 0.584 +- 0.0180.921 +- 0.016
SonicParanoid_default 826 +- 5415726 0.551 +- 0.0200.907 +- 0.020
SonicParanoid_most 1153 +- 6319502 0.586 +- 0.0170.919 +- 0.016
SonicParanoid_sensitive 1077 +- 6118629 0.585 +- 0.0170.923 +- 0.016

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 completed tree samples (out of 50k trials)Number of predicted pairwise ortholog relations Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
BBH 1181 +- 675675032 0.878 +- 0.0190.268 +- 0.010
Broccoli_1.1 1263 +- 6917222075 0.890 +- 0.0170.296 +- 0.010
eggNOG 453 +- 427813959 0.892 +- 0.0290.281 +- 0.017
Ensembl_Compara 2386 +- 9334069421 0.901 +- 0.0120.3390 +- 0.0087
Hieranoid2 711 +- 529644226 0.848 +- 0.0260.260 +- 0.013
InParanoid 1403 +- 7212568693 0.849 +- 0.0190.2527 +- 0.0093
OMA_GETHOGs_2.0 1096 +- 64198154959 0.832 +- 0.0220.251 +- 0.011
OMA_Groups_2.0 183 +- 263404204 0.863 +- 0.0500.255 +- 0.025
OMA_Pairs_2.0 490 +- 438844020 0.865 +- 0.0300.266 +- 0.016
OrthoFinder_2_BLAST__DendroBLAST_ 1274 +- 6914990262 0.874 +- 0.0180.283 +- 0.010
OrthoFinder_2_BLAST__MSA 1194 +- 6714108708 0.892 +- 0.0180.281 +- 0.010
OrthoFinder_2_Defaults_DIAMOND__MSA 1230 +- 6812180481 0.871 +- 0.0190.274 +- 0.010
OrthoFinder_2_DIAMOND__MSA 1086 +- 6413040690 0.882 +- 0.0190.285 +- 0.011
OrthoInspector_3.0 2014 +- 8610848200 0.863 +- 0.0150.2626 +- 0.0077
OrthoMCL 2552 +- 9614842444 0.9306 +- 0.00990.3967 +- 0.0094
PANTHER_14.1_all 1596 +- 7716419904 0.878 +- 0.0160.2871 +- 0.0094
PANTHER_14.1_LDO_only 736 +- 534824919 0.857 +- 0.0250.249 +- 0.012
Proteinortho_5.16b 679 +- 514932294 0.875 +- 0.0250.304 +- 0.016
Proteinortho_6.0.13 442 +- 414518412 0.871 +- 0.0310.264 +- 0.017
RSD 924 +- 595770391 0.881 +- 0.0210.281 +- 0.012
SonicParanoid_default 1155 +- 6613298118 0.839 +- 0.0210.248 +- 0.010
SonicParanoid_most 1837 +- 8214579191 0.848 +- 0.0160.2615 +- 0.0084
SonicParanoid_sensitive 1643 +- 7814189929 0.848 +- 0.0170.2622 +- 0.0089

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 predicted pairwise ortholog relationsNumber of completed tree samples (out of 50k trials) Avg Robinson-Foulds distance (genetree, exp. speciestree)Fraction of incorrect trees
BBH 46094153120 +- 106 0.2367 +- 0.00620.816 +- 0.014
Broccoli_1.1 150798225749 +- 140 0.2495 +- 0.00650.833 +- 0.013
eggNOG 70238133984 +- 119 0.2346 +- 0.00620.813 +- 0.014
Ensembl_Compara 294897207037 +- 152 0.2903 +- 0.00710.874 +- 0.012
Hieranoid2 85670703335 +- 109 0.2198 +- 0.00600.801 +- 0.014
InParanoid 106938353853 +- 117 0.2211 +- 0.00600.800 +- 0.014
OMA_GETHOGs_2.0 1909039723518 +- 112 0.2429 +- 0.00650.823 +- 0.014
OMA_Groups_2.0 29778261000 +- 61 0.2086 +- 0.00990.782 +- 0.026
OMA_Pairs_2.0 79436962318 +- 92 0.2126 +- 0.00690.777 +- 0.017
OrthoFinder_2_BLAST__DendroBLAST_ 130276565651 +- 139 0.2527 +- 0.00640.840 +- 0.013
OrthoFinder_2_BLAST__MSA 123259295774 +- 140 0.2468 +- 0.00620.836 +- 0.013
OrthoFinder_2_Defaults_DIAMOND__MSA 105769495348 +- 135 0.2400 +- 0.00640.826 +- 0.014
OrthoFinder_2_DIAMOND__MSA 114588825791 +- 140 0.2501 +- 0.00640.836 +- 0.013
OrthoInspector_3.0 89518125500 +- 137 0.2281 +- 0.00620.803 +- 0.014
OrthoMCL 129222976510 +- 147 0.3442 +- 0.00870.886 +- 0.011
PANTHER_14.1_all 142065835651 +- 139 0.2640 +- 0.00680.841 +- 0.013
PANTHER_14.1_LDO_only 42045133505 +- 112 0.2338 +- 0.00630.805 +- 0.014
Proteinortho_5.16b 42181302183 +- 90 0.2582 +- 0.00810.825 +- 0.016
Proteinortho_6.0.13 39528831974 +- 85 0.2361 +- 0.00810.809 +- 0.017
RSD 46201402203 +- 90 0.2505 +- 0.00800.826 +- 0.016
SonicParanoid_default 115818193879 +- 117 0.2317 +- 0.00600.830 +- 0.013
SonicParanoid_most 121732684890 +- 130 0.2304 +- 0.00630.807 +- 0.014
SonicParanoid_sensitive 119754804627 +- 127 0.2309 +- 0.00620.812 +- 0.014

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) Avg Robinson-Foulds distance (genetree, exp. speciestree)Fraction of incorrect trees
BBH 109644114720 +- 200 0.2405 +- 0.00610.893 +- 0.011
Broccoli_1.1 240554322058 +- 218 0.2509 +- 0.00620.907 +- 0.010
eggNOG 140116522388 +- 218 0.2314 +- 0.00560.892 +- 0.011
Ensembl_Compara 337824024567 +- 219 0.2419 +- 0.00570.896 +- 0.011
Hieranoid2 149008217806 +- 210 0.2266 +- 0.00560.887 +- 0.011
InParanoid 164126717975 +- 210 0.2289 +- 0.00580.890 +- 0.011
OMA_GETHOGs_2.0 689490018340 +- 211 0.2400 +- 0.00620.899 +- 0.011
OMA_Groups_2.0 102527713864 +- 196 0.2231 +- 0.00550.887 +- 0.011
OMA_Pairs_2.0 268848917958 +- 210 0.2340 +- 0.00590.895 +- 0.011
OrthoFinder_2_BLAST__DendroBLAST_ 206569024224 +- 219 0.2376 +- 0.00560.899 +- 0.011
OrthoFinder_2_BLAST__MSA 213933526356 +- 219 0.2438 +- 0.00580.898 +- 0.011
OrthoFinder_2_Defaults_DIAMOND__MSA 167454524337 +- 219 0.2365 +- 0.00570.893 +- 0.011
OrthoFinder_2_DIAMOND__MSA 188415526241 +- 219 0.2411 +- 0.00580.903 +- 0.011
OrthoInspector_3.0 136452720053 +- 215 0.2304 +- 0.00570.888 +- 0.011
OrthoMCL 391098028449 +- 217 0.473 +- 0.0120.9453 +- 0.0081
PANTHER_14.1_all 232705120976 +- 216 0.2462 +- 0.00600.897 +- 0.011
PANTHER_14.1_LDO_only 105708916654 +- 207 0.2278 +- 0.00560.891 +- 0.011
Proteinortho_5.16b 127369615975 +- 204 0.359 +- 0.0100.9227 +- 0.0096
Proteinortho_6.0.13 123634117002 +- 208 0.2954 +- 0.00880.892 +- 0.011
RSD 108339013397 +- 194 0.2570 +- 0.00630.914 +- 0.010
SonicParanoid_default 184948519826 +- 214 0.2277 +- 0.00540.903 +- 0.011
SonicParanoid_most 183927519763 +- 214 0.2266 +- 0.00550.893 +- 0.011
SonicParanoid_sensitive 185118519725 +- 214 0.2340 +- 0.00570.900 +- 0.011

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 23651410483 +- 178 0.689 +- 0.0170.2779 +- 0.0087
Broccoli_1.1 30599513845 +- 196 0.704 +- 0.0160.2958 +- 0.0091
eggNOG 26486912105 +- 188 0.679 +- 0.0170.2761 +- 0.0087
Ensembl_Compara 33007512491 +- 190 0.703 +- 0.0160.2938 +- 0.0091
Hieranoid2 24954110581 +- 179 0.654 +- 0.0170.2552 +- 0.0084
InParanoid 2542369991 +- 175 0.666 +- 0.0170.2615 +- 0.0086
OMA_GETHOGs_2.0 2054336210 +- 145 0.634 +- 0.0170.2413 +- 0.0082
OMA_Groups_2.0 1400484046 +- 120 0.599 +- 0.0180.2226 +- 0.0079
OMA_Pairs_2.0 2020056444 +- 147 0.634 +- 0.0170.2442 +- 0.0084
OrthoFinder_2_BLAST__DendroBLAST_ 33577414296 +- 198 0.700 +- 0.0160.2898 +- 0.0089
OrthoFinder_2_BLAST__MSA 33399514190 +- 198 0.694 +- 0.0160.2857 +- 0.0088
OrthoFinder_2_Defaults_DIAMOND__MSA 31946213768 +- 196 0.692 +- 0.0170.2908 +- 0.0091
OrthoFinder_2_DIAMOND__MSA 32495114209 +- 198 0.697 +- 0.0160.2945 +- 0.0091
OrthoInspector_3.0 28950813091 +- 193 0.686 +- 0.0170.2811 +- 0.0089
OrthoMCL 34081314760 +- 200 0.742 +- 0.0160.352 +- 0.010
PANTHER_14.1_all 35436813458 +- 194 0.729 +- 0.0160.3166 +- 0.0093
PANTHER_14.1_LDO_only 22700911750 +- 186 0.673 +- 0.0170.2731 +- 0.0088
Proteinortho_5.16b 1704915690 +- 139 0.671 +- 0.0170.2669 +- 0.0088
Proteinortho_6.0.13 1746046133 +- 144 0.632 +- 0.0170.2418 +- 0.0083
RSD 2285568859 +- 167 0.688 +- 0.0170.2798 +- 0.0088
SonicParanoid_default 24423610179 +- 176 0.676 +- 0.0170.2663 +- 0.0085
SonicParanoid_most 27310412368 +- 189 0.690 +- 0.0170.2706 +- 0.0084
SonicParanoid_sensitive 26931411902 +- 187 0.673 +- 0.0170.2626 +- 0.0084

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
BBHaaa 0.565 +- 0.031 0.922 +- 0.034
Broccoli_1.1 0.749 +- 0.031 0.955 +- 0.028
eggNOG 0.646 +- 0.030 0.946 +- 0.037
Ensembl_Compara 0.743 +- 0.031 0.923 +- 0.028
Hieranoid2 0.675 +- 0.032 0.956 +- 0.028
InParanoid 0.698 +- 0.032 0.953 +- 0.027
OMA_GETHOGs_2.0 0.674 +- 0.032 0.943 +- 0.028
OMA_Groups_2.0 0.487 +- 0.033 0.949 +- 0.035
OMA_Pairs_2.0 0.652 +- 0.032 0.939 +- 0.028
OrthoFinder_2_BLAST__DendroBLAST_ 0.815 +- 0.029 0.950 +- 0.026
OrthoFinder_2_BLAST__MSA 0.839 +- 0.029 0.948 +- 0.026
OrthoFinder_2_Defaults_DIAMOND__MSA 0.794 +- 0.030 0.958 +- 0.029
OrthoFinder_2_DIAMOND__MSA 0.780 +- 0.030 0.943 +- 0.030
OrthoInspector_3.0 0.746 +- 0.031 0.932 +- 0.027
OrthoMCL 0.725 +- 0.030 0.861 +- 0.029
PANTHER_14.1_all 0.783 +- 0.030 0.936 +- 0.028
PANTHER_14.1_LDO_only 0.550 +- 0.032 0.954 +- 0.035
Proteinortho_5.16b 0.581 +- 0.032 0.909 +- 0.032
Proteinortho_6.0.13 0.561 +- 0.033 0.932 +- 0.029
RSD 0.528 +- 0.032 0.918 +- 0.036
SonicParanoid_default 0.678 +- 0.032 0.953 +- 0.028
SonicParanoid_most 0.715 +- 0.032 0.945 +- 0.027
SonicParanoid_sensitive 0.702 +- 0.032 0.947 +- 0.027

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 0.4765 +- 0.0062 0.9534 +- 0.0037
Broccoli_1.1 0.6919 +- 0.0058 0.9485 +- 0.0032
eggNOG 0.5867 +- 0.0062 0.9522 +- 0.0034
Ensembl_Compara 0.6552 +- 0.0059 0.8187 +- 0.0054
Hieranoid2 0.6267 +- 0.0060 0.9344 +- 0.0038
InParanoid 0.6427 +- 0.0060 0.9362 +- 0.0037
OMA_GETHOGs_2.0 0.6428 +- 0.0060 0.8355 +- 0.0053
OMA_Groups_2.0 0.3868 +- 0.0061 0.9513 +- 0.0042
OMA_Pairs_2.0 0.5643 +- 0.0062 0.9179 +- 0.0044
OrthoFinder_2_BLAST__DendroBLAST_ 0.6965 +- 0.0057 0.9267 +- 0.0038
OrthoFinder_2_BLAST__MSA 0.6895 +- 0.0058 0.9252 +- 0.0038
OrthoFinder_2_Defaults_DIAMOND__MSA 0.6981 +- 0.0057 0.9243 +- 0.0038
OrthoFinder_2_DIAMOND__MSA 0.6838 +- 0.0058 0.9244 +- 0.0038
OrthoInspector_3.0 0.6781 +- 0.0058 0.9321 +- 0.0037
OrthoMCL 0.6879 +- 0.0058 0.8225 +- 0.0052
PANTHER_14.1_all 0.6956 +- 0.0057 0.8820 +- 0.0045
PANTHER_14.1_LDO_only 0.4406 +- 0.0062 0.9547 +- 0.0038
Proteinortho_5.16b 0.4765 +- 0.0062 0.9039 +- 0.0051
Proteinortho_6.0.13 0.4664 +- 0.0062 0.9243 +- 0.0047
RSD 0.4211 +- 0.0062 0.9498 +- 0.0041
SonicParanoid_default 0.6438 +- 0.0060 0.9361 +- 0.0037
SonicParanoid_most 0.6639 +- 0.0059 0.9359 +- 0.0036
SonicParanoid_sensitive 0.6609 +- 0.0059 0.9372 +- 0.0036

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 85240 0.5067 +- 0.0016
Broccoli_1.1 174302 0.4749 +- 0.0011
eggNOG 102266 0.5009 +- 0.0014
Ensembl_Compara 351359 0.44556 +- 0.00074
Hieranoid2 130511 0.4878 +- 0.0013
InParanoid 154587 0.4848 +- 0.0012
OMA_GETHOGs_2.0 936482 0.41161 +- 0.00042
OMA_Groups_2.0 58918 0.5135 +- 0.0019
OMA_Pairs_2.0 105205 0.4967 +- 0.0014
OrthoFinder_2_BLAST__DendroBLAST_ 154358 0.4852 +- 0.0012
OrthoFinder_2_BLAST__MSA 150884 0.4888 +- 0.0012
OrthoFinder_2_Defaults_DIAMOND__MSA 145550 0.4892 +- 0.0012
OrthoFinder_2_DIAMOND__MSA 147339 0.4886 +- 0.0012
OrthoInspector_3.0 155915 0.4871 +- 0.0011
OrthoMCL 167084 0.4844 +- 0.0011
PANTHER_14.1_all 189576 0.4761 +- 0.0010
PANTHER_14.1_LDO_only 73809 0.5113 +- 0.0017
Proteinortho_5.16b 83898 0.5084 +- 0.0016
Proteinortho_6.0.13 76201 0.5085 +- 0.0017
RSD 78139 0.5052 +- 0.0016
SonicParanoid_default 160390 0.4821 +- 0.0011
SonicParanoid_most 166884 0.4839 +- 0.0011
SonicParanoid_sensitive 164967 0.4842 +- 0.0011

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 146109 0.95032 +- 0.00078
Broccoli_1.1 200997 0.91239 +- 0.00088
eggNOG 135421 0.95945 +- 0.00073
Ensembl_Compara 298884 0.85597 +- 0.00094
Hieranoid2 162184 0.94602 +- 0.00076
InParanoid 203148 0.91339 +- 0.00086
OMA_GETHOGs_2.0 492301 0.75774 +- 0.00082
OMA_Groups_2.0 96947 0.97511 +- 0.00068
OMA_Pairs_2.0 149980 0.95719 +- 0.00071
OrthoFinder_2_BLAST__DendroBLAST_ 187870 0.93012 +- 0.00081
OrthoFinder_2_BLAST__MSA 178820 0.93313 +- 0.00086
OrthoFinder_2_Defaults_DIAMOND__MSA 184194 0.93791 +- 0.00079
OrthoFinder_2_DIAMOND__MSA 182653 0.94157 +- 0.00076
OrthoInspector_3.0 204100 0.92526 +- 0.00080
OrthoMCL 222495 0.92485 +- 0.00080
PANTHER_14.1_all 200000 0.92842 +- 0.00082
PANTHER_14.1_LDO_only 112068 0.96601 +- 0.00073
Proteinortho_5.16b 141722 0.95954 +- 0.00071
Proteinortho_6.0.13 127057 0.97210 +- 0.00060
RSD 139053 0.94503 +- 0.00085
SonicParanoid_default 189541 0.91999 +- 0.00085
SonicParanoid_most 212649 0.91151 +- 0.00085
SonicParanoid_sensitive 207822 0.91462 +- 0.00084