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Table 1 Phylogenetic resolution of various models in SIV.

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

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)

  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.