Table 1.
Overview of the main differences between simulation scenarios. Each simulation was run until a specific number of tips (
) was reached.
| Scenario | Transmission parameters |
Number of simulated transmission trees | Number of sampled tips | Bayesian inference |
|---|---|---|---|---|
| 1 |
|
5 |
or
|
and s inferred independently for each transmission tree |
| 2 |
|
5 |
|
and s inferred independently for each transmission tree |
| 3 |
|
5 |
|
and s inferred independently for each transmission tree |
| 4 |
|
6 |
|
and s inferred jointly for trees with  and jointly for trees with 
|
| 5 |
|
6 |
or
|
and s inferred jointly for trees with  and jointly for trees with 
|
| 6 |
|
36 |
or
|
and s inferred jointly for trees with  and jointly for trees with 
|
| 7 |
|
6 |
|
and s inferred jointly for trees with  and jointly for trees with 
|
| 8 |
|
6 |
or
|
and s inferred jointly for trees with  and jointly for trees with 
|
| 9 |
|
10 |
|
and s inferred independently for each transmission tree |
| 10 |
|
10 |
|
and s inferred jointly for trees with  and jointly for trees with 
|