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Table 3 Tree-ignorant 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
  MI NMI RMI SCA MIP   
  pα p > α pα p > α pα p > α pα p > α pα p > α χ 2 pvalue
(i,i+3) 2 51 9 44 0 53 10 43 11 42 17.98 1.24 × 10-3
(i,i+4) 32 21 41 12 1 52 36 17 18 35 79.28 2.48 × 10 -16
(B) Randomized Tetrapod Myoglobin
  MI NMI RMI SCA MIP   
  pα p > α pα p > α pα p > α pα p > α pα p > α χ 2 pvalue
(i,i+3) 4 49 0 53 0 53 0 53 0 53 16.25 2.71 × 10 -3
(i,i+4) 0 53 0 53 0 53 0 53 1 52 4.02 4.04 × 10-1
(C) Chordate Myosin
  MI NMI RMI SCA MIP   
  pα p > α pα p > α pα p > α pα p > α pα p > α χ 2 pvalue
(i,i+3) 51 2 46 7 38 15 40 13 46 7 14.83 5.08 × 10 -3
(i,i+4) 52 1 44 9 26 27 44 9 43 10 41.30 2.33 × 10 -8
(D) Randomized Chordate Myosin
  MI NMI RMI SCA MIP   
  pα p > α pα p > α pα p > α pα p > α pα p > α χ 2 pvalue
(i,i+3) 5 48 18 35 4 49 2 51 27 26 53.30 7.38 × 10 -11
(i,i+4) 0 53 0 53 0 53 0 53 0 53 n/a n/a
  1. χ2 goodness-of-fit tests comparing the performance of tree-ignorant methods for detecting alpha helix periodicity at (i, i + 3) and (i, i + 4). Bolded rows highlight statistically significant χ2 results, indicating a difference between the methods. Bold counts in these rows highlight which method achieved the highest ratio of significant to insignificant scores. Counts are calculated using the empirically determined optimal SCA cutoff for each positive control data point. SCA cutoff is 0.9 for A-B row 1, 0.8 for A-B row 2, 0.4 for C-D row 1, and 0.6 for C-D row 2. α = 0.01.