Skip to main content

Table 1 Phylogenetic resolution of various models in SIV.

From: Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

Model  # 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)
  1. 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.