Power analyses of the type II LRTs

A.% 2lt (CA)% lt (CA)% 0.5lt (CA)
2l0(CA I)0.722.517.32
l0(CA I)0.351.193.34
0.5l0(CA I)0.170.581.60
B.l0% α= 1.15% α= ∞
CA I0.21401.190.82
CA II0.13320.720.49
CA III0.29531.671.18
  • Percentages are the probabilities of observing by chance (P) a fixed amino acid difference between one CA subfamily and the two others. (A) Power analysis for CA I vs. II and III, given varying lengths of the stem for the former subfamily [l0(CA I) = 0.2140 replacements/site] vs. total tree [lt(CA) = 3.3730 replacements/site]. (B) Power analysis for each CA subfamily, with and without a gamma distribution (α= 1.15 and ∞, respectively). The 1.15 estimate is the ML value for the CAs under the Jones, Taylor, and Thornton model with a gamma correction (Jones et al. 1992; Yang 1996).