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Table 2 Tree-aware methods compared on myoglobin and myosin.

From: Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

(A) Tetrapod Myoglobin
  GCTMPCA (ε = 0.70) LnLCorr99 LnLCorr07 Ancestral States CoMap   
  pα p > α pα p > α pα p > α pα p > α pα p > α χ 2 pvalue
(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   
  pα p > α pα p > α pα p > α pα p > α pα p > α χ 2 pvalue
(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   
  pα p > α pα p > α pα p > α pα p > α pα p > α χ 2 pvalue
(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   
  pα p > α pα p > α pα p > α pα p > α pα p > α χ 2 pvalue
(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
  1. χ2 goodness-of-fit tests comparing the performance of tree-aware 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 tree-aware methods with the single exception being (i, i+ 4) in myosin, where AS and CoMap out-perform LnLCorr99. Data is not presented on the myosin alignment for tree-aware 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.