Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

Table 1 Phylogenetic resolution of various models in SIV.

Model	Â	# sites		#/6 with PP			Estimates
Model	Â	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 Â 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.

ISSN: 2730-7182