Where one study disagrees with what other studies report for the same models, and what we are doing to resolve each case.
These are automatic leads, not findings of error. Each release, a check compares how every study ranks the models it shares with other studies. It flags a study that reverses the order the others agree on, or whose gap to a shared reference model lies well outside theirs. Different tasks, populations or metrics often explain a flag.
A flag never hides a result. Flagged results stay in every table, page and download, marked Contested. A result is withheld only when a reviewer marks it disputed.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks LRT above MetaLR in 15 of 17 comparisons; 2 of 2 other studies rank MetaLR above LRT.
2 papers rank MetaLR above LRT in 12 of their 13 comparisons and LRT higher in 1. Comprehensive assessment… ranks LRT above MetaLR in 15 of its 20 comparisons and MetaLR higher in 2; 3 are ties.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks FATHMM-XF above CADD in 10 of 10 comparisons; 2 of 2 other studies rank CADD above FATHMM-XF.
2 papers rank CADD above FATHMM-XF in all 12 comparisons that are not ties (1 is a tie). Comprehensive assessment… ranks FATHMM-XF above CADD in all 10 of its comparisons.
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks MVP above ESM-1b in 2 of 2 comparisons; 2 of 2 other studies rank ESM-1b above MVP.
2 papers rank ESM-1b above MVP in all 13 of their comparisons. Brandes et al. 2023 ranks MVP above ESM-1b in all 2 comparisons that are not ties (2 are ties).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks GERP above DANN in 5 of 6 comparisons; 2 of 2 other studies rank DANN above GERP.
2 papers rank DANN above GERP in all 12 comparisons that are not ties (1 is a tie). Clinical likelihood ratios and balanced… ranks GERP above DANN in 5 of its 6 comparisons and DANN higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks REVEL above ClinPred in 6 of 7 comparisons; 2 of 2 other studies rank ClinPred above REVEL.
3 papers rank ClinPred above REVEL in 10 of their 12 comparisons and REVEL higher in 1; 1 is a tie. Livesey and Marsh 2025 ranks REVEL above ClinPred in 6 of its 7 comparisons and ClinPred higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-1b above BayesDel in 6 of 7 comparisons; 2 of 2 other studies rank BayesDel above ESM-1b.
2 papers rank BayesDel above ESM-1b in all 10 of their comparisons. Livesey and Marsh 2025 ranks ESM-1b above BayesDel in 6 of its 7 comparisons and BayesDel higher in 1.
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks MVP above REVEL in 4 of 5 comparisons; 3 of 3 other studies rank REVEL above MVP.
3 papers rank REVEL above MVP in all 19 comparisons that are not ties (4 are ties). Clinical likelihood ratios and balanced… ranks MVP above REVEL in 4 of its 5 comparisons and REVEL higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutationAssessor above Eigen in 6 of 7 comparisons; 3 of 3 other studies rank Eigen above MutationAssessor.
3 papers rank Eigen above MutationAssessor in 17 of their 22 comparisons and MutationAssessor higher in 1; 4 are ties. Livesey and Marsh 2025 ranks MutationAssessor above Eigen in 6 of its 7 comparisons and Eigen higher in 1.
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks ESM-1b above EVE in 6 of 6 comparisons; 2 of 2 other studies rank EVE above ESM-1b.
2 papers rank EVE above ESM-1b in 22 of their 26 comparisons and ESM-1b higher in 1; 3 are ties. Brandes et al. 2023 ranks ESM-1b above EVE in all 6 comparisons that are not ties (2 are ties).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutationAssessor above FATHMM-MKL in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-MKL above MutationAssessor.
2 papers rank FATHMM-MKL above MutationAssessor in 19 of their 25 comparisons and MutationAssessor higher in 6. Livesey and Marsh 2025 ranks MutationAssessor above FATHMM-MKL in all 7 of its comparisons.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks GenoCanyon above SIFT in 6 of 8 comparisons; 3 of 3 other studies rank SIFT above GenoCanyon.
3 papers rank SIFT above GenoCanyon in 14 of their 16 comparisons and GenoCanyon higher in 1; 1 is a tie. Comprehensive assessment… ranks GenoCanyon above SIFT in 6 of its 10 comparisons and SIFT higher in 2; 2 are ties.
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks MetaLR above ESM-1b in 2 of 2 comparisons; 2 of 2 other studies rank ESM-1b above MetaLR.
2 papers rank ESM-1b above MetaLR in all 13 of their comparisons. Brandes et al. 2023 ranks MetaLR above ESM-1b in all 2 comparisons that are not ties (2 are ties).
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks MetaSVM above ESM-1b in 2 of 2 comparisons; 2 of 2 other studies rank ESM-1b above MetaSVM.
2 papers rank ESM-1b above MetaSVM in all 13 of their comparisons. Brandes et al. 2023 ranks MetaSVM above ESM-1b in all 2 comparisons that are not ties (2 are ties).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks M-CAP above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above M-CAP.
2 papers rank FATHMM-XF above M-CAP in 22 of their 26 comparisons and M-CAP higher in 3; 1 is a tie. Livesey and Marsh 2025 ranks M-CAP above FATHMM-XF in all 7 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaLR above FATHMM-MKL in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-MKL above MetaLR.
2 papers rank FATHMM-MKL above MetaLR in 18 of their 25 comparisons and MetaLR higher in 5; 2 are ties. Livesey and Marsh 2025 ranks MetaLR above FATHMM-MKL in all 7 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaLR above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above MetaLR.
2 papers rank FATHMM-XF above MetaLR in 22 of their 26 comparisons and MetaLR higher in 3; 1 is a tie. Livesey and Marsh 2025 ranks MetaLR above FATHMM-XF in all 7 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaSVM above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above MetaSVM.
2 papers rank FATHMM-XF above MetaSVM in 22 of their 26 comparisons and MetaSVM higher in 4. Livesey and Marsh 2025 ranks MetaSVM above FATHMM-XF in all 7 of its comparisons.
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks BayesDel above REVEL in 6 of 6 comparisons; 2 of 2 other studies rank REVEL above BayesDel.
3 papers rank REVEL above BayesDel in 11 of their 14 comparisons and BayesDel higher in 2; 1 is a tie. Of those papers, ProteinGym ranks BayesDel higher on its own (1 of 1). An openly licensed benchmark… ranks BayesDel above REVEL in all 6 of its comparisons.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks LRT above MetaSVM in 16 of 20 comparisons; 2 of 2 other studies rank MetaSVM above LRT.
2 papers rank MetaSVM above LRT in 12 of their 13 comparisons and LRT higher in 1. Comprehensive assessment… ranks LRT above MetaSVM in 16 of its 20 comparisons and MetaSVM higher in 4.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-1b above MutPred in 6 of 7 comparisons; 2 of 2 other studies rank MutPred above ESM-1b.
3 papers rank MutPred above ESM-1b in 8 of their 11 comparisons and ESM-1b higher in 1; 2 are ties. Of those papers, ProteinGym ranks ESM-1b higher on its own (1 of 1). Livesey and Marsh 2025 ranks ESM-1b above MutPred in 6 of its 7 comparisons and MutPred higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutationAssessor above MPC in 6 of 7 comparisons; 2 of 2 other studies rank MPC above MutationAssessor.
2 papers rank MPC above MutationAssessor in all 16 of their comparisons. Livesey and Marsh 2025 ranks MutationAssessor above MPC in 6 of its 7 comparisons and MPC higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PolyPhen-2 above MVP in 6 of 6 comparisons; 3 of 3 other studies rank MVP above PolyPhen-2.
3 papers rank MVP above PolyPhen-2 in 18 of their 21 comparisons and PolyPhen-2 higher in 2; 1 is a tie. Livesey and Marsh 2025 ranks PolyPhen-2 above MVP in all 6 of its comparisons.
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks GenoCanyon above phyloP in 3 of 3 comparisons; 2 of 2 other studies rank phyloP above GenoCanyon.
2 papers rank phyloP above GenoCanyon in 11 of their 13 comparisons and GenoCanyon higher in 1; 1 is a tie. Brandes et al. 2023 ranks GenoCanyon above phyloP in all 3 comparisons that are not ties (1 is a tie).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-1b above VEST4 in 6 of 7 comparisons; 2 of 2 other studies rank VEST4 above ESM-1b.
2 papers rank VEST4 above ESM-1b in 7 of their 10 comparisons and ESM-1b higher in 1; 2 are ties. Livesey and Marsh 2025 ranks ESM-1b above VEST4 in 6 of its 7 comparisons and VEST4 higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutationAssessor above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above MutationAssessor.
2 papers rank FATHMM-XF above MutationAssessor in 21 of their 26 comparisons and MutationAssessor higher in 5. Livesey and Marsh 2025 ranks MutationAssessor above FATHMM-XF in all 7 of its comparisons.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks GenoCanyon above MetaSVM in 6 of 8 comparisons; 2 of 2 other studies rank MetaSVM above GenoCanyon.
2 papers rank MetaSVM above GenoCanyon in 12 of their 13 comparisons and GenoCanyon higher in 1. Comprehensive assessment… ranks GenoCanyon above MetaSVM in 6 of its 10 comparisons and MetaSVM higher in 2; 2 are ties.
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks SiPhy above phyloP in 3 of 4 comparisons; 2 of 2 other studies rank phyloP above SiPhy.
2 papers rank phyloP above SiPhy in all 13 of their comparisons. Brandes et al. 2023 ranks SiPhy above phyloP in 3 of its 4 comparisons and phyloP higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks SIFT above FATHMM-XF in 6 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above SIFT.
2 papers rank FATHMM-XF above SIFT in 25 of their 26 comparisons and SIFT higher in 1. Livesey and Marsh 2025 ranks SIFT above FATHMM-XF in 6 of its 7 comparisons and FATHMM-XF higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PolyPhen-2 above FATHMM-XF in 6 of 6 comparisons; 2 of 2 other studies rank FATHMM-XF above PolyPhen-2.
2 papers rank FATHMM-XF above PolyPhen-2 in 20 of their 26 comparisons and PolyPhen-2 higher in 1; 5 are ties. Livesey and Marsh 2025 ranks PolyPhen-2 above FATHMM-XF in all 6 of its comparisons.
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks SiPhy above GERP in 4 of 4 comparisons; 2 of 2 other studies rank GERP above SiPhy.
2 papers rank GERP above SiPhy in 11 of their 13 comparisons and SiPhy higher in 1; 1 is a tie. Brandes et al. 2023 ranks SiPhy above GERP in all 4 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above DEOGEN2 in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks DEOGEN2 above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank DEOGEN2 above MutFormer in 6 of their 13 comparisons and MutFormer higher in 7. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks VESPAl above CARP in 15 of 19 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks CARP above VESPAl in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank CARP above VESPAl in 10 of their 25 comparisons and VESPAl higher in 15. Of those papers, ProteinGym ranks VESPAl higher on its own (15 of 19).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks MetaLR above SuSPect in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks SuSPect above MetaLR in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank SuSPect above MetaLR in 7 of their 13 comparisons and MetaLR higher in 5; 1 is a tie. Of those papers, Clinical likelihood ratios and balanced… ranks MetaLR higher on its own (4 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks VARITY above MetaRNN in 6 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MetaRNN above VARITY in 3 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
3 papers rank MetaRNN above VARITY in 5 of their 14 comparisons and VARITY higher in 7; 2 are ties. Of those papers, Livesey and Marsh 2025 ranks VARITY higher on its own (6 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above MPC in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MPC above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MPC above MutFormer in 6 of their 13 comparisons and MutFormer higher in 7. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks Tranception above ESM-1b in 15 of 19 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-1b above Tranception in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM-1b above Tranception in 11 of their 26 comparisons and Tranception higher in 15. Of those papers, ProteinGym ranks Tranception higher on its own (15 of 19).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks FATHMM-MKL above SNAP2 in 3 of 4 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks SNAP2 above FATHMM-MKL in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank SNAP2 above FATHMM-MKL in 8 of their 12 comparisons and FATHMM-MKL higher in 3; 1 is a tie. Of those papers, Clinical likelihood ratios and balanced… ranks FATHMM-MKL higher on its own (3 of 5).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above SIFT in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks SIFT above MutFormer in 3 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above SIFT in 8 of their 13 comparisons and SIFT higher in 3; 2 are ties. Of those papers, An openly licensed benchmark… ranks SIFT higher on its own (3 of 6).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks VESPA above CARP in 18 of 19 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks CARP above VESPA in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank CARP above VESPA in 7 of their 25 comparisons and VESPA higher in 18. Of those papers, ProteinGym ranks VESPA higher on its own (18 of 19).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks MetaSVM above Condel in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above MetaSVM in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above MetaSVM in 8 of their 13 comparisons and MetaSVM higher in 4; 1 is a tie. Of those papers, Clinical likelihood ratios and balanced… ranks MetaSVM higher on its own (4 of 6).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks Tranception above ESM-2 in 16 of 18 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-2 above Tranception in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM-2 above Tranception in 9 of their 26 comparisons and Tranception higher in 16; 1 is a tie. Of those papers, ProteinGym ranks Tranception higher on its own (16 of 19).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks DeepSequence above ESM-1v in 13 of 17 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-1v above DeepSequence in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM-1v above DeepSequence in 10 of their 26 comparisons and DeepSequence higher in 14; 2 are ties. Of those papers, ProteinGym ranks DeepSequence higher on its own (13 of 19).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks SIFT above Condel in 5 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above SIFT in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above SIFT in 7 of their 12 comparisons and SIFT higher in 5. Of those papers, Clinical likelihood ratios and balanced… ranks SIFT higher on its own (5 of 5).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks ESM-1b above CARP in 14 of 18 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks CARP above ESM-1b in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank CARP above ESM-1b in 10 of their 25 comparisons and ESM-1b higher in 14; 1 is a tie. Of those papers, ProteinGym ranks ESM-1b higher on its own (14 of 19).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks Tranception above CARP in 19 of 19 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks CARP above Tranception in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank CARP above Tranception in 6 of their 25 comparisons and Tranception higher in 19. Of those papers, ProteinGym ranks Tranception higher on its own (19 of 19).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaRNN above MutScore in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutScore above MetaRNN in 3 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MetaRNN above MutScore in 8 of their 13 comparisons and MutScore higher in 3; 2 are ties. Of those papers, An openly licensed benchmark… ranks MutScore higher on its own (3 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above PolyPhen-2 in 6 of 6 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks PolyPhen-2 above MutFormer in 5 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above PolyPhen-2 in 7 of their 12 comparisons and PolyPhen-2 higher in 5. Of those papers, An openly licensed benchmark… ranks PolyPhen-2 higher on its own (5 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaRNN above ClinPred in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks ClinPred above MetaRNN in 2 of 2 comparisons. No other study gives a verdict, so neither is the outlier.
3 papers rank ClinPred above MetaRNN in 2 of their 14 comparisons and MetaRNN higher in 7; 5 are ties. Of those papers, Livesey and Marsh 2025 ranks MetaRNN higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks VARITY above MutScore in 6 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutScore above VARITY in 4 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutScore above VARITY in 5 of their 13 comparisons and VARITY higher in 6; 2 are ties. Of those papers, Livesey and Marsh 2025 ranks VARITY higher on its own (6 of 7).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks VESPA above DeepSequence in 13 of 17 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks DeepSequence above VESPA in 5 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank DeepSequence above VESPA in 9 of their 26 comparisons and VESPA higher in 14; 3 are ties. Of those papers, ProteinGym ranks VESPA higher on its own (13 of 19).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks MetaSVM above SuSPect in 5 of 6 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks SuSPect above MetaSVM in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank SuSPect above MetaSVM in 8 of their 13 comparisons and MetaSVM higher in 5. Of those papers, Clinical likelihood ratios and balanced… ranks MetaSVM higher on its own (5 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above REVEL in 6 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks REVEL above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above REVEL in 6 of their 13 comparisons and REVEL higher in 7. Of those papers, An openly licensed benchmark… ranks REVEL higher on its own (6 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PHACTboost above MutScore in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutScore above PHACTboost in 5 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutScore above PHACTboost in 5 of their 13 comparisons and PHACTboost higher in 7; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks PHACTboost higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above PROVEAN in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks PROVEAN above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above PROVEAN in 7 of their 13 comparisons and PROVEAN higher in 6. Of those papers, An openly licensed benchmark… ranks PROVEAN higher on its own (6 of 6).
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) ranks CADD above ESM-2 in 14 of 14 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-2 above CADD in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM-2 above CADD in 6 of their 21 comparisons and CADD higher in 15. Of those papers, Genome modelling and design across all… ranks CADD higher on its own (14 of 14).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above ESM-1b in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks ESM-1b above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above ESM-1b in 7 of their 13 comparisons and ESM-1b higher in 6. Of those papers, An openly licensed benchmark… ranks ESM-1b higher on its own (6 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above M-CAP in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks M-CAP above MutFormer in 4 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank M-CAP above MutFormer in 4 of their 13 comparisons and MutFormer higher in 8; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks MVP above Condel in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above MVP in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above MVP in 7 of their 12 comparisons and MVP higher in 5. Of those papers, Clinical likelihood ratios and balanced… ranks MVP higher on its own (4 of 5).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above FATHMM-XF in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks FATHMM-XF above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank FATHMM-XF above MutFormer in 6 of their 13 comparisons and MutFormer higher in 7. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks PolyPhen-2 above Condel in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above PolyPhen-2 in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above PolyPhen-2 in 7 of their 12 comparisons and PolyPhen-2 higher in 4; 1 is a tie. Of those papers, Clinical likelihood ratios and balanced… ranks PolyPhen-2 higher on its own (4 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above BayesDel in 6 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks BayesDel above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above BayesDel in 6 of their 13 comparisons and BayesDel higher in 7. Of those papers, An openly licensed benchmark… ranks BayesDel higher on its own (6 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PHACTboost above BayesDel in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks BayesDel above PHACTboost in 4 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank PHACTboost above BayesDel in 8 of their 13 comparisons and BayesDel higher in 4; 1 is a tie. Of those papers, An openly licensed benchmark… ranks BayesDel higher on its own (4 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks VARITY above ClinPred in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks ClinPred above VARITY in 4 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
3 papers rank ClinPred above VARITY in 5 of their 14 comparisons and VARITY higher in 7; 2 are ties. Of those papers, Livesey and Marsh 2025 ranks VARITY higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above MVP in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MVP above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above MVP in 7 of their 13 comparisons and MVP higher in 6. Of those papers, An openly licensed benchmark… ranks MVP higher on its own (6 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above ClinPred in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks ClinPred above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ClinPred above MutFormer in 6 of their 13 comparisons and MutFormer higher in 7. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PHACTboost above ClinPred in 6 of 6 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks ClinPred above PHACTboost in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ClinPred above PHACTboost in 6 of their 13 comparisons and PHACTboost higher in 6; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks PHACTboost higher on its own (6 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above MutationAssessor in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutationAssessor above MutFormer in 5 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutationAssessor above MutFormer in 5 of their 13 comparisons and MutFormer higher in 7; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks FATHMM-MKL above Condel in 5 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above FATHMM-MKL in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above FATHMM-MKL in 7 of their 12 comparisons and FATHMM-MKL higher in 5. Of those papers, Clinical likelihood ratios and balanced… ranks FATHMM-MKL higher on its own (5 of 5).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above MetaSVM in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MetaSVM above MutFormer in 4 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MetaSVM above MutFormer in 4 of their 13 comparisons and MutFormer higher in 8; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above MutPred in 6 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutPred above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above MutPred in 6 of their 13 comparisons and MutPred higher in 7. Of those papers, An openly licensed benchmark… ranks MutPred higher on its own (6 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above phyloP in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks phyloP above MutFormer in 4 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above phyloP in 8 of their 13 comparisons and phyloP higher in 4; 1 is a tie. Of those papers, An openly licensed benchmark… ranks phyloP higher on its own (4 of 6).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks FATHMM-MKL above BayesDel in 3 of 4 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks BayesDel above FATHMM-MKL in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank FATHMM-MKL above BayesDel in 3 of their 12 comparisons and BayesDel higher in 8; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks BayesDel higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks REVEL above MutScore in 6 of 6 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutScore above REVEL in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutScore above REVEL in 6 of their 13 comparisons and REVEL higher in 6; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks REVEL higher on its own (6 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above PrimateAI in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks PrimateAI above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above PrimateAI in 7 of their 13 comparisons and PrimateAI higher in 6. Of those papers, An openly licensed benchmark… ranks PrimateAI higher on its own (6 of 6).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks MSA Transformer above ESM-1v in 16 of 19 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-1v above MSA Transformer in 5 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM-1v above MSA Transformer in 8 of their 25 comparisons and MSA Transformer higher in 16; 1 is a tie. Of those papers, ProteinGym ranks MSA Transformer higher on its own (16 of 19).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks Tranception above EVmutation in 15 of 18 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks EVmutation above Tranception in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank EVmutation above Tranception in 10 of their 26 comparisons and Tranception higher in 15; 1 is a tie. Of those papers, ProteinGym ranks Tranception higher on its own (15 of 19).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks Tranception above VESPAl in 17 of 18 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks VESPAl above Tranception in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Tranception above VESPAl in 18 of their 26 comparisons and VESPAl higher in 7; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks VESPAl higher on its own (6 of 7).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks Tranception above ESM-1v in 14 of 17 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-1v above Tranception in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM-1v above Tranception in 10 of their 26 comparisons and Tranception higher in 14; 2 are ties. Of those papers, ProteinGym ranks Tranception higher on its own (14 of 19).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above Eigen in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks Eigen above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Eigen above MutFormer in 6 of their 13 comparisons and MutFormer higher in 7. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks Tranception above ProGen2 in 19 of 19 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ProGen2 above Tranception in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ProGen2 above Tranception in 6 of their 26 comparisons and Tranception higher in 19; 1 is a tie. Of those papers, ProteinGym ranks Tranception higher on its own (19 of 20).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks EVmutation above CARP in 15 of 19 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks CARP above EVmutation in 5 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank EVmutation above CARP in 16 of their 25 comparisons and CARP higher in 9. Of those papers, Livesey and Marsh 2025 ranks CARP higher on its own (5 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above VEST4 in 6 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks VEST4 above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above VEST4 in 6 of their 13 comparisons and VEST4 higher in 7. Of those papers, An openly licensed benchmark… ranks VEST4 higher on its own (6 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaLR above LIST-S2 in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks LIST-S2 above MetaLR in 4 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank LIST-S2 above MetaLR in 4 of their 13 comparisons and MetaLR higher in 8; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks MetaLR higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-1b above MutScore in 6 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutScore above ESM-1b in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutScore above ESM-1b in 7 of their 13 comparisons and ESM-1b higher in 6. Of those papers, Livesey and Marsh 2025 ranks ESM-1b higher on its own (6 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks M-CAP above LIST-S2 in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks LIST-S2 above M-CAP in 5 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank LIST-S2 above M-CAP in 5 of their 13 comparisons and M-CAP higher in 8. Of those papers, Livesey and Marsh 2025 ranks M-CAP higher on its own (7 of 7).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks SIFT above PANTHER in 3 of 4 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PANTHER above SIFT in 5 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank PANTHER above SIFT in 6 of their 11 comparisons and SIFT higher in 4; 1 is a tie. Of those papers, Clinical likelihood ratios and balanced… ranks SIFT higher on its own (3 of 5).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks CADD above Condel in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above CADD in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above CADD in 7 of their 12 comparisons and CADD higher in 5. Of those papers, Clinical likelihood ratios and balanced… ranks CADD higher on its own (4 of 5).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above MutScore in 6 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutScore above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above MutScore in 6 of their 13 comparisons and MutScore higher in 7. Of those papers, An openly licensed benchmark… ranks MutScore higher on its own (6 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaSVM above LIST-S2 in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks LIST-S2 above MetaSVM in 3 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank LIST-S2 above MetaSVM in 3 of their 13 comparisons and MetaSVM higher in 8; 2 are ties. Of those papers, Livesey and Marsh 2025 ranks MetaSVM higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above CADD in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks CADD above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank CADD above MutFormer in 6 of their 13 comparisons and MutFormer higher in 7. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).