Public Results 2020




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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)
Domainoid+ 13982 +- 131400464 0.0983 +- 0.00490.0434 +- 0.0023
Ensembl_Compara 13880 +- 132830691 0.1581 +- 0.00610.0710 +- 0.0029
Hieranoid_2 11227 +- 140337534 0.0808 +- 0.00500.0366 +- 0.0024
InParanoid_Xenfix 13147 +- 135364800 0.0807 +- 0.00470.0353 +- 0.0022
OMA_GETHOGs 7430 +- 135323874 0.0824 +- 0.00630.0388 +- 0.0031
OMA_Groups 7745 +- 136208368 0.0760 +- 0.00590.0372 +- 0.0031
OMA_Pairs 10357 +- 141332081 0.0842 +- 0.00530.0386 +- 0.0026
OrthoFinder_MSA_v2.5.2 13283 +- 135381685 0.1229 +- 0.00560.0548 +- 0.0027
OrthoInspector 3 12138 +- 138316624 0.0901 +- 0.00510.0399 +- 0.0024
OrthoMCL 11117 +- 140723546 0.3972 +- 0.00910.2683 +- 0.0069
PANTHER_16_all 14444 +- 129474683 0.1302 +- 0.00550.0568 +- 0.0026
PANTHER__16__LDO__only 7484 +- 135231682 0.0836 +- 0.00630.0378 +- 0.0031
sonicparanoid 12338 +- 138387531 0.0861 +- 0.00490.0383 +- 0.0023
sonicparanoid-fast 11737 +- 139372284 0.0810 +- 0.00490.0370 +- 0.0024
sonicparanoid-mostsensitive 12805 +- 136397545 0.0872 +- 0.00490.0381 +- 0.0023
sonicparanoid-sens 12671 +- 137391205 0.0860 +- 0.00490.0380 +- 0.0023

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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)
Domainoid+ 9743 +- 168115556 0.6567 +- 0.00940.3289 +- 0.0055
Ensembl_Compara 10349 +- 172147702 0.6855 +- 0.00890.3636 +- 0.0058
Hieranoid_2 9084 +- 164106979 0.6478 +- 0.00980.3221 +- 0.0057
InParanoid_Xenfix 9054 +- 164106943 0.6420 +- 0.00990.3214 +- 0.0057
OMA_GETHOGs 5713 +- 13780347 0.610 +- 0.0130.2999 +- 0.0072
OMA_Groups 5118 +- 13160667 0.586 +- 0.0130.2906 +- 0.0077
OMA_Pairs 6683 +- 14685553 0.607 +- 0.0120.3004 +- 0.0066
OrthoFinder_MSA_v2.5.2 11235 +- 176141479 0.6771 +- 0.00860.3463 +- 0.0053
OrthoInspector 3 9996 +- 170116800 0.6571 +- 0.00930.3286 +- 0.0055
OrthoMCL 10937 +- 175147095 0.7231 +- 0.00840.4098 +- 0.0060
PANTHER_16_all 11661 +- 178157949 0.6954 +- 0.00840.3739 +- 0.0055
PANTHER__16__LDO__only 9518 +- 16798061 0.6650 +- 0.00950.3332 +- 0.0056
sonicparanoid 8680 +- 162103713 0.641 +- 0.0100.3175 +- 0.0058
sonicparanoid-fast 7652 +- 15493208 0.629 +- 0.0110.3070 +- 0.0061
sonicparanoid-mostsensitive 9797 +- 169114948 0.6567 +- 0.00940.3264 +- 0.0055
sonicparanoid-sens 9513 +- 167112138 0.6585 +- 0.00950.3259 +- 0.0055

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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)
Domainoid+ 1165 +- 6319875 0.921 +- 0.0160.590 +- 0.017
Ensembl_Compara 1130 +- 6226255 0.921 +- 0.0160.600 +- 0.018
Hieranoid_2 1034 +- 6016831 0.906 +- 0.0180.566 +- 0.018
InParanoid_Xenfix 1072 +- 6118071 0.920 +- 0.0160.575 +- 0.017
OMA_GETHOGs 1124 +- 6230677 0.913 +- 0.0170.588 +- 0.018
OMA_Groups 587 +- 4610745 0.876 +- 0.0270.516 +- 0.024
OMA_Pairs 871 +- 5520018 0.897 +- 0.0200.551 +- 0.020
OrthoFinder_MSA_v2.5.2 1017 +- 5920605 0.915 +- 0.0170.573 +- 0.018
OrthoInspector 3 1129 +- 6218151 0.928 +- 0.0150.590 +- 0.017
OrthoMCL 1619 +- 7228012 0.944 +- 0.0110.661 +- 0.015
PANTHER_16_all 1166 +- 6328146 0.937 +- 0.0140.619 +- 0.017
PANTHER__16__LDO__only 912 +- 5612388 0.908 +- 0.0190.557 +- 0.019
sonicparanoid 862 +- 5516053 0.907 +- 0.0190.553 +- 0.020
sonicparanoid-fast 661 +- 4913727 0.903 +- 0.0230.545 +- 0.022
sonicparanoid-mostsensitive 1131 +- 6219201 0.922 +- 0.0160.587 +- 0.017
sonicparanoid-sens 1053 +- 6018378 0.922 +- 0.0160.579 +- 0.018

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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)
Domainoid+ 1861 +- 8314706070 0.872 +- 0.0150.2676 +- 0.0081
Ensembl_Compara 2145 +- 8932536136 0.911 +- 0.0120.3421 +- 0.0090
Hieranoid_2 866 +- 579993418 0.842 +- 0.0240.261 +- 0.012
InParanoid_Xenfix 1433 +- 7312698014 0.829 +- 0.0200.2453 +- 0.0093
OMA_GETHOGs 470 +- 4248750279 0.838 +- 0.0330.243 +- 0.016
OMA_Groups 186 +- 273177904 0.817 +- 0.0560.240 +- 0.026
OMA_Pairs 554 +- 467608191 0.832 +- 0.0310.248 +- 0.015
OrthoFinder_MSA_v2.5.2 981 +- 6112030296 0.861 +- 0.0220.278 +- 0.012
OrthoInspector 3 1655 +- 788910498 0.855 +- 0.0170.2627 +- 0.0088
OrthoMCL 2577 +- 9714874362 0.9399 +- 0.00920.4079 +- 0.0096
PANTHER_16_all 1641 +- 7815757449 0.881 +- 0.0160.2893 +- 0.0093
PANTHER__16__LDO__only 781 +- 544564744 0.864 +- 0.0240.260 +- 0.012
sonicparanoid 1223 +- 6813622049 0.841 +- 0.0210.2456 +- 0.0096
sonicparanoid-fast 865 +- 5712799684 0.838 +- 0.0250.238 +- 0.011
sonicparanoid-mostsensitive 1743 +- 8014422398 0.863 +- 0.0160.2647 +- 0.0085
sonicparanoid-sens 1590 +- 7714072092 0.848 +- 0.0180.2601 +- 0.0091

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 Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
Domainoid+ 4751 +- 12912497038 0.818 +- 0.0140.2369 +- 0.0063
Ensembl_Compara 6694 +- 14928074031 0.874 +- 0.0120.3009 +- 0.0073
Hieranoid_2 3776 +- 1168829243 0.798 +- 0.0140.2285 +- 0.0062
InParanoid_Xenfix 3832 +- 11710842303 0.806 +- 0.0140.2251 +- 0.0060
OMA_GETHOGs 2908 +- 10347888937 0.815 +- 0.0140.2341 +- 0.0063
OMA_Groups 1017 +- 622758038 0.760 +- 0.0260.201 +- 0.010
OMA_Pairs 2220 +- 906721847 0.784 +- 0.0170.2162 +- 0.0071
OrthoFinder_MSA_v2.5.2 5653 +- 13910505892 0.834 +- 0.0130.2490 +- 0.0064
OrthoInspector 3 5005 +- 1327410732 0.819 +- 0.0140.2337 +- 0.0061
OrthoMCL 6520 +- 14812957517 0.885 +- 0.0110.3399 +- 0.0085
PANTHER_16_all 5796 +- 14013624033 0.840 +- 0.0130.2643 +- 0.0069
PANTHER__16__LDO__only 3475 +- 1113940648 0.814 +- 0.0140.2337 +- 0.0063
sonicparanoid 3908 +- 11811922812 0.803 +- 0.0140.2256 +- 0.0060
sonicparanoid-fast 3156 +- 10711495034 0.808 +- 0.0140.2298 +- 0.0062
sonicparanoid-mostsensitive 4734 +- 12812102352 0.817 +- 0.0140.2299 +- 0.0062
sonicparanoid-sens 4670 +- 12811954912 0.794 +- 0.0140.2244 +- 0.0062

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 Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
Domainoid+ 24253 +- 2192133475 0.9230 +- 0.00950.2505 +- 0.0057
Ensembl_Compara 22627 +- 2183093070 0.9287 +- 0.00920.2625 +- 0.0061
Hieranoid_2 19624 +- 2141645831 0.9193 +- 0.00980.2410 +- 0.0056
InParanoid_Xenfix 19514 +- 2141873928 0.912 +- 0.0100.2380 +- 0.0055
OMA_GETHOGs 17690 +- 2101663819 0.9187 +- 0.00980.2432 +- 0.0058
OMA_Groups 14238 +- 198883901 0.904 +- 0.0110.2328 +- 0.0055
OMA_Pairs 18836 +- 2121731922 0.9227 +- 0.00960.2444 +- 0.0057
OrthoFinder_MSA_v2.5.2 28102 +- 2171550014 0.916 +- 0.0120.2496 +- 0.0067
OrthoInspector 3 21910 +- 2171152080 0.912 +- 0.0100.2449 +- 0.0057
OrthoMCL 30221 +- 2143624493 0.9537 +- 0.00750.461 +- 0.011
PANTHER_16_all 23133 +- 2191866631 0.914 +- 0.0100.2587 +- 0.0061
PANTHER__16__LDO__only 18764 +- 212917626 0.9163 +- 0.00990.2470 +- 0.0059
sonicparanoid 21730 +- 2172042472 0.9187 +- 0.00980.2407 +- 0.0057
sonicparanoid-fast 21541 +- 2172057594 0.915 +- 0.0100.2422 +- 0.0057
sonicparanoid-mostsensitive 22040 +- 2181992657 0.9197 +- 0.00970.2447 +- 0.0057
sonicparanoid-sens 22079 +- 2181991237 0.9160 +- 0.00990.2448 +- 0.0056

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 Fraction of incorrect treesAvg Robinson-Foulds distance (genetree, exp. speciestree)
Domainoid+ 11604 +- 185274254 0.683 +- 0.0170.2692 +- 0.0085
Ensembl_Compara 12357 +- 189329207 0.706 +- 0.0160.3001 +- 0.0092
Hieranoid_2 10821 +- 180250360 0.658 +- 0.0170.2590 +- 0.0085
InParanoid_Xenfix 9870 +- 174254208 0.671 +- 0.0170.2628 +- 0.0085
OMA_GETHOGs 6616 +- 149192809 0.630 +- 0.0170.2407 +- 0.0082
OMA_Groups 3957 +- 118140239 0.606 +- 0.0170.2237 +- 0.0079
OMA_Pairs 6474 +- 147202009 0.638 +- 0.0170.2392 +- 0.0081
OrthoFinder_MSA_v2.5.2 14411 +- 199327013 0.691 +- 0.0210.289 +- 0.011
OrthoInspector 3 12608 +- 190276085 0.667 +- 0.0170.2642 +- 0.0086
OrthoMCL 14887 +- 200341033 0.745 +- 0.0160.347 +- 0.010
PANTHER_16_all 13687 +- 195360549 0.720 +- 0.0160.3054 +- 0.0091
PANTHER__16__LDO__only 11844 +- 186229521 0.695 +- 0.0160.2842 +- 0.0089
sonicparanoid 10424 +- 178244709 0.690 +- 0.0170.2690 +- 0.0084
sonicparanoid-fast 8842 +- 167219173 0.660 +- 0.0170.2552 +- 0.0083
sonicparanoid-mostsensitive 12532 +- 190271333 0.685 +- 0.0170.2778 +- 0.0088
sonicparanoid-sens 11882 +- 187264796 0.664 +- 0.0170.2599 +- 0.0085

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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