Table 1.
Prediction performance of PETcofold on simulated sequence data
| Scaling factor | Mean branch length | ℛ(int) | CBP | Mean MCC |
|---|---|---|---|---|
| 1 | 0.03 | 0.486 | 0.832 | 0.505 |
| 5 | 0.15 | 0.665 | 1.818 | 0.677 |
| 10 | 0.3 | 0.699 | 2.182 | 0.717 |
| 25 | 0.75 | 0.732 | 2.550 | 0.743 |
| 50 | 1.5 | 0.775 | 2.755 | 0.773 |
| 75 | 0.75 | 0.791 | 2.858 | 0.783 |
| 100 | 3.0 | 0.801 | 2.908 | 0.790 |
| 150 | 4.5 | 0.822 | 2.988 | 0.802 |
| 200 | 6.0 | 0.839 | 3.040 | 0.821 |
Scaling factor multiplies each branch length of the phylogenetic tree. Mean branch length denotes the mean of the mean branch lengths for all 32 phylogenetic trees. ℛ(int) denotes the mean base pair probability at the interaction sites (calculated by Pfold). CBP denotes the average number of compensatory interaction base pair exchanges in the simulated sequence data. MCC evaluates only the interaction. PETcofold was called with parameters δ = 0.9, γ = 0.1 and option -noLP to forbid lonely base pairs.