Public Results 2018




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 10438 +- 142253964 0.0481 +- 0.00290.1038 +- 0.0059
eggNOG 10514 +- 142309229 0.0541 +- 0.00310.1145 +- 0.0061
Ensembl_Compara 14771 +- 130919469 0.0657 +- 0.00270.1489 +- 0.0057
Hieranoid2 11268 +- 142370057 0.0355 +- 0.00240.0783 +- 0.0050
InParanoid 13265 +- 137372972 0.0334 +- 0.00210.0754 +- 0.0045
OMA_GETHOGs_2.0 9022 +- 141979210 0.0440 +- 0.00300.0957 +- 0.0061
OMA_Groups_2.0 7797 +- 137221155 0.0383 +- 0.00310.0775 +- 0.0059
OMA_Pairs_2.0 10485 +- 142388087 0.0399 +- 0.00260.0865 +- 0.0054
OrthoFinder_2_BLAST__DendroBLAST_ 14015 +- 134440806 0.0533 +- 0.00260.1195 +- 0.0054
OrthoFinder_2_BLAST__MSA 14362 +- 132448830 0.0607 +- 0.00270.1371 +- 0.0056
OrthoFinder_2_Defaults_DIAMOND__MSA 13366 +- 137397504 0.0503 +- 0.00260.1126 +- 0.0054
OrthoFinder_2_DIAMOND__MSA 13584 +- 136422920 0.0564 +- 0.00270.1257 +- 0.0056
OrthoInspector_3.0 12686 +- 139353832 0.0423 +- 0.00240.0946 +- 0.0051
PANTHER_14.1_all 14632 +- 131503821 0.0538 +- 0.00250.1201 +- 0.0053
PANTHER_14.1_LDO_only 7589 +- 136244550 0.0375 +- 0.00300.0822 +- 0.0062
Proteinortho_6.0.13_with-isoform 7248 +- 135229170 0.0387 +- 0.00320.0815 +- 0.0063
RSD 11637 +- 141250748 0.0717 +- 0.00340.1501 +- 0.0065
SonicParanoid_default 12406 +- 140401992 0.0373 +- 0.00230.0825 +- 0.0048
SonicParanoid_most 12914 +- 138415668 0.0380 +- 0.00230.0858 +- 0.0048
SonicParanoid_sensitive 12867 +- 138415850 0.0362 +- 0.00220.0817 +- 0.0047
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 9703 +- 168101823 0.3314 +- 0.00560.6567 +- 0.0094
eggNOG 9509 +- 167112392 0.3286 +- 0.00560.6595 +- 0.0095
Ensembl_Compara 10346 +- 172147706 0.3668 +- 0.00580.6856 +- 0.0089
Hieranoid2 9045 +- 164106844 0.3178 +- 0.00570.6448 +- 0.0099
InParanoid 9054 +- 164106949 0.3177 +- 0.00570.6427 +- 0.0099
OMA_GETHOGs_2.0 5459 +- 13586840 0.3026 +- 0.00750.607 +- 0.013
OMA_Groups_2.0 5153 +- 13160642 0.2893 +- 0.00760.584 +- 0.013
OMA_Pairs_2.0 6683 +- 14685561 0.3046 +- 0.00670.615 +- 0.012
OrthoFinder_2_BLAST__DendroBLAST_ 11342 +- 177143997 0.3463 +- 0.00530.6770 +- 0.0086
OrthoFinder_2_BLAST__MSA 11291 +- 177143606 0.3457 +- 0.00530.6733 +- 0.0087
OrthoFinder_2_Defaults_DIAMOND__MSA 10912 +- 175137482 0.3383 +- 0.00530.6666 +- 0.0088
OrthoFinder_2_DIAMOND__MSA 10932 +- 175140626 0.3432 +- 0.00530.6724 +- 0.0088
OrthoInspector_3.0 10373 +- 172122628 0.3366 +- 0.00540.6679 +- 0.0091
PANTHER_14.1_all 11603 +- 178154677 0.3776 +- 0.00550.6985 +- 0.0084
PANTHER_14.1_LDO_only 9440 +- 16796998 0.3332 +- 0.00570.6637 +- 0.0095
Proteinortho_6.0.13_with-isoform 5523 +- 13565591 0.2912 +- 0.00730.591 +- 0.013
RSD 9180 +- 16598374 0.3349 +- 0.00590.6563 +- 0.0097
SonicParanoid_default 8647 +- 161103590 0.3190 +- 0.00580.647 +- 0.010
SonicParanoid_most 9879 +- 169115613 0.3317 +- 0.00550.6626 +- 0.0093
SonicParanoid_sensitive 9629 +- 168114959 0.3253 +- 0.00550.6552 +- 0.0095
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
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
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_6.0.13_with-isoform 827 +- 5411958 0.542 +- 0.0200.898 +- 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
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 1181 +- 675675032 0.268 +- 0.0100.878 +- 0.019
eggNOG 453 +- 427813959 0.281 +- 0.0170.892 +- 0.029
Ensembl_Compara 2386 +- 9334069421 0.3390 +- 0.00870.901 +- 0.012
Hieranoid2 711 +- 529644226 0.260 +- 0.0130.848 +- 0.026
InParanoid 1403 +- 7212568693 0.2527 +- 0.00930.849 +- 0.019
OMA_GETHOGs_2.0 1096 +- 64198154959 0.251 +- 0.0110.832 +- 0.022
OMA_Groups_2.0 183 +- 263404204 0.255 +- 0.0250.863 +- 0.050
OMA_Pairs_2.0 490 +- 438844020 0.266 +- 0.0160.865 +- 0.030
OrthoFinder_2_BLAST__DendroBLAST_ 1274 +- 6914990262 0.283 +- 0.0100.874 +- 0.018
OrthoFinder_2_BLAST__MSA 1194 +- 6714108708 0.281 +- 0.0100.892 +- 0.018
OrthoFinder_2_Defaults_DIAMOND__MSA 1230 +- 6812180481 0.274 +- 0.0100.871 +- 0.019
OrthoFinder_2_DIAMOND__MSA 1086 +- 6413040690 0.285 +- 0.0110.882 +- 0.019
OrthoInspector_3.0 2014 +- 8610848200 0.2626 +- 0.00770.863 +- 0.015
PANTHER_14.1_all 1596 +- 7716419904 0.2871 +- 0.00940.878 +- 0.016
PANTHER_14.1_LDO_only 736 +- 534824919 0.249 +- 0.0120.857 +- 0.025
Proteinortho_6.0.13_with-isoform 03523573 n/an/a
RSD 924 +- 595770391 0.281 +- 0.0120.881 +- 0.021
SonicParanoid_default 1155 +- 6613298118 0.248 +- 0.0100.839 +- 0.021
SonicParanoid_most 1837 +- 8214579191 0.2615 +- 0.00840.848 +- 0.016
SonicParanoid_sensitive 1643 +- 7814189929 0.2622 +- 0.00890.848 +- 0.017
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 3120 +- 1064609415 0.2367 +- 0.00620.816 +- 0.014
eggNOG 3984 +- 1197023813 0.2346 +- 0.00620.813 +- 0.014
Ensembl_Compara 7037 +- 15229489720 0.2903 +- 0.00710.874 +- 0.012
Hieranoid2 3335 +- 1098567070 0.2198 +- 0.00600.801 +- 0.014
InParanoid 3853 +- 11710693835 0.2211 +- 0.00600.800 +- 0.014
OMA_GETHOGs_2.0 3518 +- 112190903972 0.2429 +- 0.00650.823 +- 0.014
OMA_Groups_2.0 1000 +- 612977826 0.2086 +- 0.00990.782 +- 0.026
OMA_Pairs_2.0 2318 +- 927943696 0.2126 +- 0.00690.777 +- 0.017
OrthoFinder_2_BLAST__DendroBLAST_ 5651 +- 13913027656 0.2527 +- 0.00640.840 +- 0.013
OrthoFinder_2_BLAST__MSA 5774 +- 14012325929 0.2468 +- 0.00620.836 +- 0.013
OrthoFinder_2_Defaults_DIAMOND__MSA 5348 +- 13510576949 0.2400 +- 0.00640.826 +- 0.014
OrthoFinder_2_DIAMOND__MSA 5791 +- 14011458882 0.2501 +- 0.00640.836 +- 0.013
OrthoInspector_3.0 5500 +- 1378951812 0.2281 +- 0.00620.803 +- 0.014
PANTHER_14.1_all 5651 +- 13914206583 0.2640 +- 0.00680.841 +- 0.013
PANTHER_14.1_LDO_only 3505 +- 1124204513 0.2338 +- 0.00630.805 +- 0.014
Proteinortho_6.0.13_with-isoform 1697 +- 793360247 0.2177 +- 0.00810.787 +- 0.020
RSD 2203 +- 904620140 0.2505 +- 0.00800.826 +- 0.016
SonicParanoid_default 3879 +- 11711581819 0.2317 +- 0.00600.830 +- 0.013
SonicParanoid_most 4890 +- 13012173268 0.2304 +- 0.00630.807 +- 0.014
SonicParanoid_sensitive 4627 +- 12711975480 0.2309 +- 0.00620.812 +- 0.014
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 14720 +- 2001096441 0.2405 +- 0.00610.893 +- 0.011
eggNOG 22388 +- 2181401165 0.2314 +- 0.00560.892 +- 0.011
Ensembl_Compara 24567 +- 2193378240 0.2419 +- 0.00570.896 +- 0.011
Hieranoid2 17806 +- 2101490082 0.2266 +- 0.00560.887 +- 0.011
InParanoid 17975 +- 2101641267 0.2289 +- 0.00580.890 +- 0.011
OMA_GETHOGs_2.0 18340 +- 2116894900 0.2400 +- 0.00620.899 +- 0.011
OMA_Groups_2.0 13864 +- 1961025277 0.2231 +- 0.00550.887 +- 0.011
OMA_Pairs_2.0 17958 +- 2102688489 0.2340 +- 0.00590.895 +- 0.011
OrthoFinder_2_BLAST__DendroBLAST_ 24224 +- 2192065690 0.2376 +- 0.00560.899 +- 0.011
OrthoFinder_2_BLAST__MSA 26356 +- 2192139335 0.2438 +- 0.00580.898 +- 0.011
OrthoFinder_2_Defaults_DIAMOND__MSA 24337 +- 2191674545 0.2365 +- 0.00570.893 +- 0.011
OrthoFinder_2_DIAMOND__MSA 26241 +- 2191884155 0.2411 +- 0.00580.903 +- 0.011
OrthoInspector_3.0 20053 +- 2151364527 0.2304 +- 0.00570.888 +- 0.011
PANTHER_14.1_all 20976 +- 2162327051 0.2462 +- 0.00600.897 +- 0.011
PANTHER_14.1_LDO_only 16654 +- 2071057089 0.2278 +- 0.00560.891 +- 0.011
Proteinortho_6.0.13_with-isoform 14113 +- 1971078384 0.2309 +- 0.00590.886 +- 0.011
RSD 13397 +- 1941083390 0.2570 +- 0.00630.914 +- 0.010
SonicParanoid_default 19826 +- 2141849485 0.2277 +- 0.00540.903 +- 0.011
SonicParanoid_most 19763 +- 2141839275 0.2266 +- 0.00550.893 +- 0.011
SonicParanoid_sensitive 19725 +- 2141851185 0.2340 +- 0.00570.900 +- 0.011
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 10483 +- 178236514 0.2779 +- 0.00870.689 +- 0.017
eggNOG 12105 +- 188264869 0.2761 +- 0.00870.679 +- 0.017
Ensembl_Compara 12491 +- 190330075 0.2938 +- 0.00910.703 +- 0.016
Hieranoid2 10581 +- 179249541 0.2552 +- 0.00840.654 +- 0.017
InParanoid 9991 +- 175254236 0.2615 +- 0.00860.666 +- 0.017
OMA_GETHOGs_2.0 6210 +- 145205433 0.2413 +- 0.00820.634 +- 0.017
OMA_Groups_2.0 4046 +- 120140048 0.2226 +- 0.00790.599 +- 0.018
OMA_Pairs_2.0 6444 +- 147202005 0.2442 +- 0.00840.634 +- 0.017
OrthoFinder_2_BLAST__DendroBLAST_ 14296 +- 198335774 0.2898 +- 0.00890.700 +- 0.016
OrthoFinder_2_BLAST__MSA 14190 +- 198333995 0.2857 +- 0.00880.694 +- 0.016
OrthoFinder_2_Defaults_DIAMOND__MSA 13768 +- 196319462 0.2908 +- 0.00910.692 +- 0.017
OrthoFinder_2_DIAMOND__MSA 14209 +- 198324951 0.2945 +- 0.00910.697 +- 0.016
OrthoInspector_3.0 13091 +- 193289508 0.2811 +- 0.00890.686 +- 0.017
PANTHER_14.1_all 13458 +- 194354368 0.3166 +- 0.00930.729 +- 0.016
PANTHER_14.1_LDO_only 11750 +- 186227009 0.2731 +- 0.00880.673 +- 0.017
Proteinortho_6.0.13_with-isoform 5218 +- 134154031 0.2359 +- 0.00810.629 +- 0.017
RSD 8859 +- 167228556 0.2798 +- 0.00880.688 +- 0.017
SonicParanoid_default 10179 +- 176244236 0.2663 +- 0.00850.676 +- 0.017
SonicParanoid_most 12368 +- 189273104 0.2706 +- 0.00840.690 +- 0.017
SonicParanoid_sensitive 11902 +- 187269314 0.2626 +- 0.00840.673 +- 0.017
Project True positive rate Positive predictive value rate
BBH 0.565 +- 0.031 0.922 +- 0.034
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
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_6.0.13_with-isoform 0.488 +- 0.032 0.943 +- 0.034
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
Project True positive rate Positive predictive value rate
BBH 0.4765 +- 0.0062 0.9534 +- 0.0037
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
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_6.0.13_with-isoform 0.4329 +- 0.0062 0.9516 +- 0.0040
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
Project Number of predicted pairwise ortholog relations Avg Schlicker similarity
BBH 85240 0.5067 +- 0.0016
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
PANTHER_14.1_all 189576 0.4761 +- 0.0010
PANTHER_14.1_LDO_only 73809 0.5113 +- 0.0017
Proteinortho_6.0.13_with-isoform 61848 0.5118 +- 0.0018
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
Project Number of predicted pairwise ortholog relations Avg Schlicker similarity
BBH 146109 0.95032 +- 0.00078
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
PANTHER_14.1_all 200000 0.92842 +- 0.00082
PANTHER_14.1_LDO_only 112068 0.96601 +- 0.00073
Proteinortho_6.0.13_with-isoform 88280 0.98526 +- 0.00052
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