Public Results 2020




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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
Domainoid+ 13982 +- 131400464 0.0434 +- 0.00230.0983 +- 0.0049
Ensembl_Compara 13880 +- 132830691 0.0710 +- 0.00290.1581 +- 0.0061
Hieranoid_2 11227 +- 140337534 0.0366 +- 0.00240.0808 +- 0.0050
InParanoid_Xenfix 13147 +- 135364800 0.0353 +- 0.00220.0807 +- 0.0047
OMA_GETHOGs 7430 +- 135323874 0.0388 +- 0.00310.0824 +- 0.0063
OMA_Groups 7745 +- 136208368 0.0372 +- 0.00310.0760 +- 0.0059
OMA_Pairs 10357 +- 141332081 0.0386 +- 0.00260.0842 +- 0.0053
OrthoFinder_MSA_v2.5.2 13283 +- 135381685 0.0548 +- 0.00270.1229 +- 0.0056
OrthoInspector 3 12138 +- 138316624 0.0399 +- 0.00240.0901 +- 0.0051
OrthoMCL 11117 +- 140723546 0.2683 +- 0.00690.3972 +- 0.0091
PANTHER_16_all 14444 +- 129474683 0.0568 +- 0.00260.1302 +- 0.0055
PANTHER__16__LDO__only 7484 +- 135231682 0.0378 +- 0.00310.0836 +- 0.0063
sonicparanoid 12338 +- 138387531 0.0383 +- 0.00230.0861 +- 0.0049
sonicparanoid-fast 11737 +- 139372284 0.0370 +- 0.00240.0810 +- 0.0049
sonicparanoid-mostsensitive 12805 +- 136397545 0.0381 +- 0.00230.0872 +- 0.0049
sonicparanoid-sens 12671 +- 137391205 0.0380 +- 0.00230.0860 +- 0.0049

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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
Domainoid+ 9743 +- 168115556 0.3289 +- 0.00550.6567 +- 0.0094
Ensembl_Compara 10349 +- 172147702 0.3636 +- 0.00580.6855 +- 0.0089
Hieranoid_2 9084 +- 164106979 0.3221 +- 0.00570.6478 +- 0.0098
InParanoid_Xenfix 9054 +- 164106943 0.3214 +- 0.00570.6420 +- 0.0099
OMA_GETHOGs 5713 +- 13780347 0.2999 +- 0.00720.610 +- 0.013
OMA_Groups 5118 +- 13160667 0.2906 +- 0.00770.586 +- 0.013
OMA_Pairs 6683 +- 14685553 0.3004 +- 0.00660.607 +- 0.012
OrthoFinder_MSA_v2.5.2 11235 +- 176141479 0.3463 +- 0.00530.6771 +- 0.0086
OrthoInspector 3 9996 +- 170116800 0.3286 +- 0.00550.6571 +- 0.0093
OrthoMCL 10937 +- 175147095 0.4098 +- 0.00600.7231 +- 0.0084
PANTHER_16_all 11661 +- 178157949 0.3739 +- 0.00550.6954 +- 0.0084
PANTHER__16__LDO__only 9518 +- 16798061 0.3332 +- 0.00560.6650 +- 0.0095
sonicparanoid 8680 +- 162103713 0.3175 +- 0.00580.641 +- 0.010
sonicparanoid-fast 7652 +- 15493208 0.3070 +- 0.00610.629 +- 0.011
sonicparanoid-mostsensitive 9797 +- 169114948 0.3264 +- 0.00550.6567 +- 0.0094
sonicparanoid-sens 9513 +- 167112138 0.3259 +- 0.00550.6585 +- 0.0095

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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
Domainoid+ 1165 +- 6319875 0.590 +- 0.0170.921 +- 0.016
Ensembl_Compara 1130 +- 6226255 0.600 +- 0.0180.921 +- 0.016
Hieranoid_2 1034 +- 6016831 0.566 +- 0.0180.906 +- 0.018
InParanoid_Xenfix 1072 +- 6118071 0.575 +- 0.0170.920 +- 0.016
OMA_GETHOGs 1124 +- 6230677 0.588 +- 0.0180.913 +- 0.017
OMA_Groups 587 +- 4610745 0.516 +- 0.0240.876 +- 0.027
OMA_Pairs 871 +- 5520018 0.551 +- 0.0200.897 +- 0.020
OrthoFinder_MSA_v2.5.2 1017 +- 5920605 0.573 +- 0.0180.915 +- 0.017
OrthoInspector 3 1129 +- 6218151 0.590 +- 0.0170.928 +- 0.015
OrthoMCL 1619 +- 7228012 0.661 +- 0.0150.944 +- 0.011
PANTHER_16_all 1166 +- 6328146 0.619 +- 0.0170.937 +- 0.014
PANTHER__16__LDO__only 912 +- 5612388 0.557 +- 0.0190.908 +- 0.019
sonicparanoid 862 +- 5516053 0.553 +- 0.0200.907 +- 0.019
sonicparanoid-fast 661 +- 4913727 0.545 +- 0.0220.903 +- 0.023
sonicparanoid-mostsensitive 1131 +- 6219201 0.587 +- 0.0170.922 +- 0.016
sonicparanoid-sens 1053 +- 6018378 0.579 +- 0.0180.922 +- 0.016

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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
Domainoid+ 1861 +- 8314706070 0.2676 +- 0.00810.872 +- 0.015
Ensembl_Compara 2145 +- 8932536136 0.3421 +- 0.00900.911 +- 0.012
Hieranoid_2 866 +- 579993418 0.261 +- 0.0120.842 +- 0.024
InParanoid_Xenfix 1433 +- 7312698014 0.2453 +- 0.00930.829 +- 0.020
OMA_GETHOGs 470 +- 4248750279 0.243 +- 0.0160.838 +- 0.033
OMA_Groups 186 +- 273177904 0.240 +- 0.0260.817 +- 0.056
OMA_Pairs 554 +- 467608191 0.248 +- 0.0150.832 +- 0.031
OrthoFinder_MSA_v2.5.2 981 +- 6112030296 0.278 +- 0.0120.861 +- 0.022
OrthoInspector 3 1655 +- 788910498 0.2627 +- 0.00880.855 +- 0.017
OrthoMCL 2577 +- 9714874362 0.4079 +- 0.00960.9399 +- 0.0092
PANTHER_16_all 1641 +- 7815757449 0.2893 +- 0.00930.881 +- 0.016
PANTHER__16__LDO__only 781 +- 544564744 0.260 +- 0.0120.864 +- 0.024
sonicparanoid 1223 +- 6813622049 0.2456 +- 0.00960.841 +- 0.021
sonicparanoid-fast 865 +- 5712799684 0.238 +- 0.0110.838 +- 0.025
sonicparanoid-mostsensitive 1743 +- 8014422398 0.2647 +- 0.00850.863 +- 0.016
sonicparanoid-sens 1590 +- 7714072092 0.2601 +- 0.00910.848 +- 0.018

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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
Domainoid+ 4751 +- 12912497038 0.2369 +- 0.00630.818 +- 0.014
Ensembl_Compara 6694 +- 14928074031 0.3009 +- 0.00730.874 +- 0.012
Hieranoid_2 3776 +- 1168829243 0.2285 +- 0.00620.798 +- 0.014
InParanoid_Xenfix 3832 +- 11710842303 0.2251 +- 0.00600.806 +- 0.014
OMA_GETHOGs 2908 +- 10347888937 0.2341 +- 0.00630.815 +- 0.014
OMA_Groups 1017 +- 622758038 0.201 +- 0.0100.760 +- 0.026
OMA_Pairs 2220 +- 906721847 0.2162 +- 0.00710.784 +- 0.017
OrthoFinder_MSA_v2.5.2 5653 +- 13910505892 0.2490 +- 0.00640.834 +- 0.013
OrthoInspector 3 5005 +- 1327410732 0.2337 +- 0.00610.819 +- 0.014
OrthoMCL 6520 +- 14812957517 0.3399 +- 0.00850.885 +- 0.011
PANTHER_16_all 5796 +- 14013624033 0.2643 +- 0.00690.840 +- 0.013
PANTHER__16__LDO__only 3475 +- 1113940648 0.2337 +- 0.00630.814 +- 0.014
sonicparanoid 3908 +- 11811922812 0.2256 +- 0.00600.803 +- 0.014
sonicparanoid-fast 3156 +- 10711495034 0.2298 +- 0.00620.808 +- 0.014
sonicparanoid-mostsensitive 4734 +- 12812102352 0.2299 +- 0.00620.817 +- 0.014
sonicparanoid-sens 4670 +- 12811954912 0.2244 +- 0.00620.794 +- 0.014

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.

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
Domainoid+ 24253 +- 2192133475 0.2505 +- 0.00570.9230 +- 0.0095
Ensembl_Compara 22627 +- 2183093070 0.2625 +- 0.00610.9287 +- 0.0092
Hieranoid_2 19624 +- 2141645831 0.2410 +- 0.00560.9193 +- 0.0098
InParanoid_Xenfix 19514 +- 2141873928 0.2380 +- 0.00550.912 +- 0.010
OMA_GETHOGs 17690 +- 2101663819 0.2432 +- 0.00580.9187 +- 0.0098
OMA_Groups 14238 +- 198883901 0.2328 +- 0.00550.904 +- 0.011
OMA_Pairs 18836 +- 2121731922 0.2444 +- 0.00570.9227 +- 0.0096
OrthoFinder_MSA_v2.5.2 28102 +- 2171550014 0.2496 +- 0.00670.916 +- 0.012
OrthoInspector 3 21910 +- 2171152080 0.2449 +- 0.00570.912 +- 0.010
OrthoMCL 30221 +- 2143624493 0.461 +- 0.0110.9537 +- 0.0075
PANTHER_16_all 23133 +- 2191866631 0.2587 +- 0.00610.914 +- 0.010
PANTHER__16__LDO__only 18764 +- 212917626 0.2470 +- 0.00590.9163 +- 0.0099
sonicparanoid 21730 +- 2172042472 0.2407 +- 0.00570.9187 +- 0.0098
sonicparanoid-fast 21541 +- 2172057594 0.2422 +- 0.00570.915 +- 0.010
sonicparanoid-mostsensitive 22040 +- 2181992657 0.2447 +- 0.00570.9197 +- 0.0097
sonicparanoid-sens 22079 +- 2181991237 0.2448 +- 0.00560.9160 +- 0.0099

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.

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
Domainoid+ 11604 +- 185274254 0.2692 +- 0.00850.683 +- 0.017
Ensembl_Compara 12357 +- 189329207 0.3001 +- 0.00920.706 +- 0.016
Hieranoid_2 10821 +- 180250360 0.2590 +- 0.00850.658 +- 0.017
InParanoid_Xenfix 9870 +- 174254208 0.2628 +- 0.00850.671 +- 0.017
OMA_GETHOGs 6616 +- 149192809 0.2407 +- 0.00820.630 +- 0.017
OMA_Groups 3957 +- 118140239 0.2237 +- 0.00790.606 +- 0.017
OMA_Pairs 6474 +- 147202009 0.2392 +- 0.00810.638 +- 0.017
OrthoFinder_MSA_v2.5.2 14411 +- 199327013 0.289 +- 0.0110.691 +- 0.021
OrthoInspector 3 12608 +- 190276085 0.2642 +- 0.00860.667 +- 0.017
OrthoMCL 14887 +- 200341033 0.347 +- 0.0100.745 +- 0.016
PANTHER_16_all 13687 +- 195360549 0.3054 +- 0.00910.720 +- 0.016
PANTHER__16__LDO__only 11844 +- 186229521 0.2842 +- 0.00890.695 +- 0.016
sonicparanoid 10424 +- 178244709 0.2690 +- 0.00840.690 +- 0.017
sonicparanoid-fast 8842 +- 167219173 0.2552 +- 0.00830.660 +- 0.017
sonicparanoid-mostsensitive 12532 +- 190271333 0.2778 +- 0.00880.685 +- 0.017
sonicparanoid-sens 11882 +- 187264796 0.2599 +- 0.00850.664 +- 0.017

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.

Project True positive rate Positive predictive value rate
Domainoid+ 0.744 +- 0.033 0.940 +- 0.029
Ensembl_Compara 0.695 +- 0.035 0.901 +- 0.034
Hieranoid_2 0.664 +- 0.034 0.945 +- 0.031
InParanoid_Xenfix 0.690 +- 0.034 0.948 +- 0.030
OMA_GETHOGs 0.681 +- 0.033 0.927 +- 0.030
OMA_Groups 0.477 +- 0.034 0.935 +- 0.038
OMA_Pairs 0.651 +- 0.034 0.929 +- 0.031
OrthoFinder_MSA_v2.5.2 0.788 +- 0.033 0.949 +- 0.029
OrthoInspector 3 0.725 +- 0.034 0.934 +- 0.030
OrthoMCL 0.702 +- 0.033 0.867 +- 0.031
PANTHER_16_all 0.761 +- 0.032 0.940 +- 0.028
PANTHER__16__LDO__only 0.533 +- 0.033 0.937 +- 0.040
sonicparanoid 0.669 +- 0.034 0.940 +- 0.030
sonicparanoid-fast 0.632 +- 0.034 0.943 +- 0.031
sonicparanoid-mostsensitive 0.703 +- 0.034 0.938 +- 0.029
sonicparanoid-sens 0.696 +- 0.034 0.942 +- 0.030

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Project True positive rate Positive predictive value rate
Domainoid+ 0.6585 +- 0.0067 0.9284 +- 0.0043
Ensembl_Compara 0.6269 +- 0.0068 0.8100 +- 0.0063
Hieranoid_2 0.6034 +- 0.0069 0.9410 +- 0.0041
InParanoid_Xenfix 0.6331 +- 0.0068 0.9351 +- 0.0042
OMA_GETHOGs 0.5581 +- 0.0070 0.9154 +- 0.0050
OMA_Groups 0.3679 +- 0.0068 0.9544 +- 0.0047
OMA_Pairs 0.5534 +- 0.0070 0.9206 +- 0.0049
OrthoFinder_MSA_v2.5.2 0.6746 +- 0.0066 0.9299 +- 0.0042
OrthoInspector 3 0.6598 +- 0.0066 0.9416 +- 0.0039
OrthoMCL 0.6822 +- 0.0065 0.8372 +- 0.0057
PANTHER_16_all 0.6753 +- 0.0066 0.8811 +- 0.0052
PANTHER__16__LDO__only 0.4222 +- 0.0069 0.9595 +- 0.0042
sonicparanoid 0.6386 +- 0.0067 0.9365 +- 0.0041
sonicparanoid-fast 0.6159 +- 0.0068 0.9359 +- 0.0042
sonicparanoid-mostsensitive 0.6590 +- 0.0067 0.9363 +- 0.0041
sonicparanoid-sens 0.6555 +- 0.0067 0.9380 +- 0.0040

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Project Number of predicted pairwise ortholog relations Avg Schlicker similarity
Domainoid+ 183591 0.4639 +- 0.0011
Ensembl_Compara 375206 0.42841 +- 0.00072
Hieranoid_2 146551 0.4684 +- 0.0012
InParanoid_Xenfix 168863 0.4658 +- 0.0011
OMA_GETHOGs 352212 0.41104 +- 0.00069
OMA_Groups 64039 0.4946 +- 0.0018
OMA_Pairs 113909 0.4749 +- 0.0014
OrthoFinder_MSA_v2.5.2 154934 0.4676 +- 0.0012
OrthoInspector 3 152202 0.4707 +- 0.0012
OrthoMCL 183578 0.4621 +- 0.0011
PANTHER_16_all 208022 0.4568 +- 0.0010
PANTHER__16__LDO__only 78794 0.4956 +- 0.0016
sonicparanoid 169199 0.4585 +- 0.0011
sonicparanoid-fast 157979 0.4588 +- 0.0011
sonicparanoid-mostsensitive 180777 0.4628 +- 0.0011
sonicparanoid-sens 179667 0.4636 +- 0.0011

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.

Project Number of predicted pairwise ortholog relations Avg Schlicker similarity
Domainoid+ 219860 0.90360 +- 0.00087
Ensembl_Compara 295273 0.84687 +- 0.00097
Hieranoid_2 169055 0.94494 +- 0.00075
InParanoid_Xenfix 205186 0.90928 +- 0.00088
OMA_GETHOGs 294320 0.82106 +- 0.00098
OMA_Groups 96646 0.97395 +- 0.00070
OMA_Pairs 149624 0.95481 +- 0.00073
OrthoFinder_MSA_v2.5.2 177405 0.93063 +- 0.00086
OrthoInspector 3 194615 0.93032 +- 0.00080
OrthoMCL 223967 0.92086 +- 0.00081
PANTHER_16_all 201349 0.92370 +- 0.00085
PANTHER__16__LDO__only 112334 0.96269 +- 0.00077
sonicparanoid 191303 0.91715 +- 0.00086
sonicparanoid-fast 174588 0.91690 +- 0.00089
sonicparanoid-mostsensitive 212599 0.90679 +- 0.00089
sonicparanoid-sens 207515 0.90998 +- 0.00088