Evidence of recombination within human alpha-papillomavirus

Angulo, Manuel; Carvajal-Rodríguez, Antonio

doi:10.1186/1743-422X-4-33

Virology Journal

Table 1 Evolutionary models for the different data sets

From: Evidence of recombination within human alpha-papillomavirus

Sequences	Nucleotide Model	Base Freqs	Rates	Invariable Sites	Rate Variation
HPV16_L1	HKY+I	A = 0.32	Ti/tv = 3.4	0.93	No
		C = 0.19
		G = 0.19
		T = 0.30
HPV16_L2	TrN+I	A = 0.31	R(a) = 1.0	0.89	No
		C = 0.22	R(b) = 6.5
		G = 0.16	R(c) = 1.0
		T = 0.31	R(d) = 1.0
			R(e) = 3.9
			R(f) = 1.0
HPV16_E6	HKY+I	A = 0.34	Ti/tv = 1.2	0.90	No
		C = 0.16
		G = 0.22
		T = 0.28
HPV16_E7	HKY+I	A = 0.31	Ti/tv= 7.0	0.95	No
		C = 0.21
		G = 0.23
		T = 0.25
GI_L1	TVM+I+G	A = 0.31	R(a) = 4.5	0.29	1.47
		C = 0.18	R(b) = 7.9
		G = 0.19	R(c) = 3.4
		T = 0.32	R(d) = 3.1
			R(e) = 7.9
			R(f) = 1.0
GI_L2	GTR+I+G	A = 0.29	R(a) = 2.4	0.17	1.67
		C = 0.21	R(b) = 4.6
		G = 0.18	R(c) = 2.8
		T = 0.32	R(d) = 1.7
			R(e) = 3.3
			R(f) = 1.0
GI_E6	TVM+I+G	A = 0.37	R(a) = 4.0	0.17	2.41
		C = 0.17	R(b) = 7.1
		G = 0.21	R(c) = 2.8
		T = 0.25	R(d) = 5.4
			R(e) = 7.1
			R(f) = 1.0
GI_E7	HKY+G	A = 0.33	Ti/tv = 1.2	0.00	0.85
		C = 0.23
		G = 0.22
		T = 0.22
GII_L1	TVM+G	A = 0.29	R(a) = 3.6	0.00	0.56
		C = 0.18	R(b) = 5.4
		G = 0.22	R(c) = 2.3
		T = 0.30	R(d) = 1.8
			R(e) = 5.4
			R(f) = 1.0
GII_L2	GTR+G	A = 0.25	R(a) = 2.3	0.00	0.84
		C = 0.24	R(b) = 4.8
		G = 0.20	R(c) = 2.6
		T = 0.30	R(d) = 1.4
			R(e) = 3.2
			R(f) = 1.0
GII_E6	TVM+G	A = 0.31	R(a) = 3.1	0.00	0.69
		C = 0.20	R(b) = 6.1
		G = 0.23	R(c) = 2.2
		T = 0.26	R(d) = 2.8
			R(e) = 6.1
			R(f) = 1.0
GII_E7	TVM+G	A = 0.31	R(a) = 3.7	0.00	1.25
		C = 0.22	R(b) = 7.5
		G = 0.24	R(c) = 3.9
		T = 0.23	R(d) = 5.0
			R(e) = 7.5
			R(f) = 1.0
GIII_L1	TVM+I+G	A = 0.24	R(a) = 2.7	0.29	0.83
		C = 0.23	R(b) = 4.8
		G = 0.22	R(c) = 1.1
		T = 0.30	R(d) = 0.9
			R(e) = 4.8
			R(f) = 1.0
GIII_L2	TVM+I+G	A = 0.22	R(a) = 1.5	0.33	1.85
		C = 0.26	R(b) = 3.1
		G = 0.22	R(c) = 1.7
		T = 0.30	R(d) = 0.7
			R(e) = 3.1
			R(f) = 1.0
GIII_E6	TrN+G	A = 0.32	R(a) = 1.0	0.00	0.68
		C = 0.22	R(b) = 2.2
		G = 0.26	R(c) = 1.0
		T = 0.20	R(d) = 1.0
			R(e) = 4.0
			R(f) = 1.0
GIII_E7	HKY+I	A = 0.27	Ti/tv = 1.1	0.32	Equal
		C = 0.20
		G = 0.30
		T = 0.23

I: Invariable sites. G: Rate variation. R(a):A-C. R(b): A-G. R(c): A-T. R(d): C-G. R(e): C-T. R(f): G-T. Ti/tv: Transition/transversion rate.

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ISSN: 1743-422X

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