Table 1.
Phylogenetic resolution of various models in SIV.
| Model | Â | # sites | #/6 with PP | Estimates | |||||
| var. | inf. | > 0.90 | > 0.95 | > 0.99 | κ | ln λ | ln ε | ||
| - Indel | Clustal W | 10 | 6 | 1 | 1 | 1 | 2.3(1.6,4.9) | - | - |
| Muscle | 12 | 7 | 4 | 3 | 0 | 2.2(1.5,4.3) | - | - | |
| MAP | 11 | 6 | 3 | 1 | 1 | 2.4(1.6,5.2) | - | - | |
| + Indel | Clustal W | 10 | 6 | 3+1 | 3+1 | 2+1 | 2.3(1.6,4.7) | -2.7(-4.5,-1.4) | -0.61(-0.93,-0.37) |
| Muscle | 12 | 7 | 3 | 3 | 2 | 2.3(1.6,4.4) | -3.5(-5.0,-2.1) | -0.92(-1.5,-0.55) | |
| MAP | 11 | 6 | 5 | 4 | 3 | 2.4(1.6,5.1) | -3.4(-5.0,-1.9) | -0.71(-1.1,-0.43) | |
| Joint | - | - | - | 4 | 3 | 3 | 2.4(1.6,5.3) | -3.4(-5.0,-1.9) | -0.71(-1.1,-0.43) |
Results are presented for the traditional sequential model (- Indel), the joint model with a fixed alignment (+ Indel), and the full joint model. The choice of a fixed alignment estimate is indicated in column  if applicable. The number of variable and informative sites is indicated under "#sites" and varies depending on the choice of alignment. The number of supported internal branches out of a possible 6 is reported at three levels of posterior probability (PP). The designation "+1" indicates that 1 of the supported branches conflicts with a branch supported under the joint model. Estimates of continuous parameters κ, ln λ, and ln ε are presented as a posterior median followed by a 95% Bayesian credible interval.