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.