Table 1.
Ortholog prediction methods InParanoid-DIAMOND, InParanoid-BLAST, the three variants of SonicParanoid, Proteinortho, OrthoFinder default and with MSA (using DIAMOND for similarity search), their runtime in hours on the Quest for Orthologs reference proteomes on a 48-thread node, the runtime in CPU hours and the number of appearances on the Pareto frontier out of the 11 Orthology benchmark service tests
| Ortholog prediction method | Runtime (hours) | Runtime (CPU hours) | Appearances on Pareto frontier |
|---|---|---|---|
| InParanoid-DIAMOND (very-sensitive) | 10.49 | 135.8 | 6 |
| InParanoid-BLAST | 166.5 | 5940.1 | 5 |
| SonicParanoid default | 2.44 | 100.8 | 2 |
| SonicParanoid sensitive | 7.23 | 325.4 | 4 |
| SonicParanoid mostSensitive | 15.68 | 725.4 | 7 |
| Proteinortho 6 | 1.69 | 74.2 | 4 |
| OrthoFinder 2 default | 2.75 | 97.8 | 7 |
| OrthoFinder 2 default+MSA | 22.07 | 749.2 | 5 |