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Table 1 Relative importance of dinucleotide parameters in improving the fit of the NFnuGTR or TFnuGTR model.

From: Pitfalls of the most commonly used models of context dependent substitution

 

NF

TF

Param

L R ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaa0aaaeaacqWHmbatcqWHsbGuaaaaaa@2E3C@

% ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaa0aaaeaacqWHLaqjaaaaaa@2CBD@ (SE)

R a n k ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaa0aaaeaacqWHsbGucqWHHbqycqWHUbGBcqWHRbWAaaaaaa@3132@ (SE)

L R ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaa0aaaeaacqWHmbatcqWHsbGuaaaaaa@2E3C@

% ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaa0aaaeaacqWHLaqjaaaaaa@2CBD@ (SE)

R a n k ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaa0aaaeaacqWHsbGucqWHHbqycqWHUbGBcqWHRbWAaaaaaa@3132@ (SE)

TG ⇔ CG

90.3

25.1 (0.3)

1.6 (0.0)

341.1

28.8 (0.2)

1.6 (0.0)

CA ⇔ CG

85.8

23.7 (0.3)

1.7 (0.0)

366.7

30.9 (0.2)

1.4 (0.0)

AT ⇔ GT

29.2

9.0 (0.2)

4.7 (0.1)

28.2

2.4 (0.1)

9.8 (0.2)

AA ⇔ GA

25.8

7.9 (0.2)

5.0 (0.1)

47.5

4.1 (0.1)

6.9 (0.2)

TT ⇔ CT

23.5

6.7 (0.1)

5.6 (0.1)

80.2

6.8 (0.1)

3.8 (0.1)

AA ⇔ AG

19.4

5.5 (0.1)

6.7 (0.1)

55.6

4.7 (0.1)

5.5 (0.1)

TT ⇔ TC

15.6

4.8 (0.1)

7.4 (0.1)

44.6

3.8 (0.1)

7.0 (0.2)

GA ⇔ GG

14.3

3.8 (0.1)

9.4 (0.3)

16.5

1.3 (0.1)

20.9 (0.6)

TC ⇔ CC

10.8

2.9 (0.1)

12.4 (0.4)

11.3

0.9 (0.1)

23.8 (0.6)

AT ⇔ AC

10.1

3.2 (0.1)

11.2 (0.3)

19.0

1.6 (0.0)

12.8 (0.2)

AG ⇔ GG

3.8

1.1 (0.1)

21.3 (0.5)

12.1

1.0 (0.1)

23.3 (0.6)

CT ⇔ GT

2.8

0.8 (0.0)

24.2 (0.5)

1.5

0.1 (0.0)

35.1 (0.4)

GC ⇔ GA

2.3

0.7 (0.0)

25.4 (0.5)

1.8

0.1 (0.0)

34.2 (0.4)

AC ⇔ GC

2.1

0.6 (0.0)

26.6 (0.5)

17.8

1.5 (0.0)

13.8 (0.3)

GC ⇔ GG

2.0

0.6 (0.0)

26.5 (0.5)

2.5

0.2 (0.0)

31.7 (0.4)

CC ⇔ CA

1.9

0.6 (0.0)

27.2 (0.5)

2.6

0.2 (0.0)

30.9 (0.5)

CT ⇔ CA

1.7

0.5 (0.0)

27.9 (0.5)

2.6

0.2 (0.0)

30.8 (0.5)

AT ⇔ AG

1.7

0.5 (0.0)

27.8 (0.5)

2.8

0.2 (0.0)

29.5 (0.4)

CT ⇔ CG

1.7

0.5 (0.0)

28.3 (0.5)

27.4

2.3 (0.1)

10.0 (0.2)

CA ⇔ GA

1.7

0.5 (0.0)

28.5 (0.5)

4.8

0.4 (0.0)

25.1 (0.4)

GT ⇔ GA

1.6

0.5 (0.0)

28.6 (0.5)

1.5

0.1 (0.0)

34.6 (0.4)

CC ⇔ CG

1.5

0.4 (0.0)

29.8 (0.5)

26.1

2.2 (0.1)

10.0 (0.2)

TT ⇔ GT

1.5

0.4 (0.0)

29.1 (0.5)

1.7

0.1 (0.0)

34.1 (0.4)

TA ⇔ TG

1.5

0.5 (0.0)

29.4 (0.5)

3.1

0.3 (0.0)

30.8 (0.5)

CT ⇔ CC

1.4

0.4 (0.0)

29.4 (0.5)

6.4

0.5 (0.0)

25.6 (0.5)

CG ⇔ AG

1.4

0.4 (0.0)

29.6 (0.5)

23.7

2.0 (0.1)

11.1 (0.2)

TC ⇔ GC

1.4

0.4 (0.0)

29.6 (0.5)

1.8

0.2 (0.0)

33.0 (0.4)

GT ⇔ GC

1.4

0.4 (0.0)

29.2 (0.5)

10.4

0.9 (0.0)

19.1 (0.4)

TT ⇔ TG

1.4

0.4 (0.0)

29.4 (0.5)

4.9

0.4 (0.0)

24.9 (0.4)

GT ⇔ GG

1.3

0.4 (0.0)

29.9 (0.5)

2.4

0.2 (0.0)

31.5 (0.4)

CG ⇔ GG

1.3

0.4 (0.0)

30.2 (0.5)

16.3

1.4 (0.0)

13.9 (0.3)

TC ⇔ AC

1.3

0.4 (0.0)

29.6 (0.5)

1.7

0.2 (0.0)

33.5 (0.4)

TA ⇔ CA

1.3

0.4 (0.0)

30.6 (0.5)

4.9

0.4 (0.0)

27.7 (0.5)

AC ⇔ AG

1.3

0.4 (0.0)

30.6 (0.5)

1.3

0.1 (0.0)

35.5 (0.4)

TC ⇔ TG

1.3

0.4 (0.0)

30.2 (0.5)

3.7

0.3 (0.0)

27.7 (0.5)

TA ⇔ AA

1.2

0.4 (0.0)

30.7 (0.5)

1.6

0.1 (0.0)

34.4 (0.4)

AT ⇔ AA

1.2

0.4 (0.0)

30.3 (0.5)

1.8

0.2 (0.0)

32.9 (0.4)

TT ⇔ AT

1.2

0.4 (0.0)

30.6 (0.5)

1.8

0.2 (0.0)

33.0 (0.4)

TG ⇔ GG

1.2

0.4 (0.0)

30.5 (0.5)

2.5

0.2 (0.0)

31.6 (0.4)

TC ⇔ TA

1.2

0.4 (0.0)

31.0 (0.5)

1.5

0.1 (0.0)

35.1 (0.4)

CT ⇔ AT

1.2

0.4 (0.0)

30.4 (0.5)

4.1

0.3 (0.0)

26.6 (0.5)

CC ⇔ GC

1.2

0.4 (0.0)

30.9 (0.5)

1.7

0.1 (0.0)

34.2 (0.4)

TT ⇔ TA

1.2

0.4 (0.0)

31.2 (0.5)

1.5

0.1 (0.0)

34.6 (0.4)

TA ⇔ GA

1.2

0.4 (0.0)

31.1 (0.5)

1.6

0.1 (0.0)

34.9 (0.4)

AC ⇔ AA

1.1

0.3 (0.0)

31.0 (0.5)

1.5

0.1 (0.0)

34.0 (0.4)

CC ⇔ AC

1.1

0.4 (0.0)

31.2 (0.5)

2.5

0.2 (0.0)

31.3 (0.5)

TG ⇔ AG

1.1

0.4 (0.0)

31.6 (0.5)

1.9

0.2 (0.0)

33.0 (0.4)

CA ⇔ AA

1.1

0.3 (0.0)

30.9 (0.5)

2.9

0.2 (0.0)

29.7 (0.5)

  1. The alternate dinucleotide models included the null model's nucleotide GTR terms plus the indicated dinucleotide parameter (Param). LR ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaa0aaaeaacqqGmbatcqqGsbGuaaaaaa@2E30@ – the per alignment mean likelihood ratio of a nuGTR + Param against the corresponding nuGTR; % ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaa0aaaeaacqGGLaqjaaaaaa@2CB8@ (SE) – the per alignment mean (and standard error) relative importance of a parameter, expressed as a percentage of the diGTR LR; Rank ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWaa0aaaeaacqqGsbGucqqGHbqycqqGUbGBcqqGRbWAaaaaaa@311A@ (SE) – the per alignment mean (and standard error) rank of the LR. Means and standard errors were estimated using the jackknife procedure. The number of alignments was 470.