Table 7.
Stepwise context reduction for the Ancestral Repeats dataset using the graph-based approach.
| Model | Contexts | Annealing | Melting | log BF |
| GTR16C | 16 (96) | [623.2; 638.2] | [645.5; 661.9] | 642.2 |
| GTR15C | 15 (90) | [658.0; 672.1] | [665.0; 682.0] | 669.2 |
| GTR14C | 14 (84) | [651.9; 668.4] | [664.3; 678.9] | 665.9 |
| GTR13C | 13 (78) | [664.9; 679.6] | [676.4; 693.1] | 678.5 |
| GTR12C | 12 (72) | [673.3; 689.1] | [685.3; 701.7] | 687.4 |
| GTR11C | 11 (66) | [682.3; 697.9] | [693.5; 710.4] | 696.0 |
| GTR10C | 10 (60) | [677.5; 693.4] | [697.5; 710.3] | 694.7 |
| GTR9C | 9 (56) | [693.7; 707.6] | [710.4; 724.6] | 709.1 |
| GTR8C | 8 (48) | [699.3; 711.7] | [712.4; 727.5] | 712.7 |
| GTR7C | 7 (42) | [686.5; 700.0] | [705.1; 719.3] | 702.7 |
| GTR6C | 6 (36) | [650.6; 663.0] | [651.2; 664.8] | 657.4 |
| GTR5C | 5 (30) | [641.4; 652.3] | [639.2; 649.2] | 645.5 |
| GTR | 1 (6) | - | - | 0 |
The stepwise context reduction using our graph-based clustering approach reveals an optimal model with 8 clusters for the Ancestral Repeats dataset (GTR8C). It attains a log Bayes Factor of 712.7 (as compared to GTR1C), a significant improvement over the full context-dependent model (GTR16C) which has twice as many parameters. This model also outperforms the 10-clusters model determined by the likelihood-based clustering approach.