(A) Tetrapod Myoglobin



GCTMPCA (ε = 0.70)

LnLCorr99

LnLCorr07

Ancestral States

CoMap
  


p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

χ
^{2}

p – value


(i,i+3)

0

53

1

5

0

7

2

51

0

9

7.51

1.11 × 10^{1}

(i,i+4)

10

43

0

6

0

7

4

49

0

9

6.75

1.50 × 10^{1}

(B) Randomized Tetrapod Myoglobin


GCTMPCA (ε = 0.70)

LnLCorr99

LnLCorr07

Ancestral States

CoMap
  

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

χ
^{2}

p – value

(i,i+3)

1

52

0

6

0

7

0

53

0

9

1.43

8.40 × 10^{1}

(i,i+4)

0

53

0

6

0

7

0

53

0

9

n/a

n/a

(C) Chordate Myosin


GCTMPCA (ε = 0.70)

LnLCorr99

LnLCorr07

Ancestral States

CoMap
  

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

χ
^{2}

p – value

(i,i+3)





5

1





41

12

8

1

0.69

7.09 × 10^{1}

(i,i+4)





2

4





48

5

8

1

14.18

8.33 × 10
^{3}

(D) Randomized Chordate Myosin


GCTMPCA (ε = 0.70)

LnLCorr99

LnLCorr07

Ancestral States

CoMap
  

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

p ≤ α

p > α

χ
^{2}

p – value

(i,i+3)





0

6





7

46

0

9

2.21

3.31 × 10^{1}

(i,i+4)





0

6





0

53

0

9

n/a

n/a

 χ^{2} goodnessoffit tests comparing the performance of treeaware methods for detecting alpha helix periodicity at (i, i + 3) and (i, i + 4). Counts are calculated for GCTMPCA with the empirically validated optimal ε = 0.70. In most cases, there is no statistically significant difference in performance between the treeaware methods with the single exception being (i, i+ 4) in myosin, where AS and CoMap outperform LnLCorr99. Data is not presented on the myosin alignment for treeaware methods which proved too computationally intensive to be practical. Counts in Table 2 can be directly compared with counts in Table 3. α = 0.01.