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Table 3 Forty three sequence positions in the EF data show the highest differences between covarion site likelihood and RAS site likelihood.

From: PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

 

Position*

Lambda**

Covarion site***

Bivar P-value****

1

34

7.280

c

<0.001

2

36

6.503

c

<0.001

3

325

6.246

c

<0.001

4

305

5.652

c

<0.001

5

138

5.458

c

<0.001

6

336

4.873

c

<0.001

7

329

4.790

c

<0.001

8

153

4.702

c

<0.001

9

327

4.632

c

0.014

10

35

4.595

c

0.022

11

123

4.438

c

0.004

12

311

4.199

c

0.003

13

189

4.034

c

0.007

14

103

3.906

c

0.001

15

69

3.726

c

0.004

16

131

3.430

c

0.002

17

256

3.256

c2

0.122

18

351

3.202

c

0.027

19

38

3.120

c1

0.043

20

51

3.073

c1

0.013

21

42

3.057

c1

0.029

22

106

2.896

c1

0.064

23

67

2.866

c

0.120

24

271

2.793

c1

0.064

25

133

2.789

c

0.045

26

144

2.700

c1

0.002

27

163

2.604

c

0.006

28

263

2.588

c

0.033

29

31

2.557

c1

0.012

30

39

2.442

c1

0.065

31

160

2.274

c

0.073

32

64

2.23

c1

0.038

33

32

2.143

c

0.147

34

82

2.116

c1

0.029

35

96

2.092

c1

0.080

36

326

2.060

c

0.021

37

178

2.047

c1

0.341

38

37

1.935

c1

0.081

39

40

1.921

c1

0.023

40

350

1.875

c1

0.071

41

355

1.818

c1

0.039

42

288

1.755656

c1

0.043

43

356

1.694422

c1

0.111

  1. * Sequence position is based on the EF alignment [24]. **Λ = ln(lcov) - ln(lras). ***c: sites were found to be covarion sites of functional or structural significance in [24]; c1: sites having typical covarion site pattern but missed in [24]; c2: site showing non-typical covarion site pattern. ****P-values from a Bivar analysis of the EF data.
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BMC Ecology and Evolution

ISSN: 2730-7182

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