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Table 1 Estimated parameters under SPR-based full tree search for datasets of 250 amino acid sites simulated based on a 17-taxa chaperonin tree with JTT + the listed models.

From: PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

Model Parameter ln likelihood # SPR CPU time
   Used in simulation PROCOV estimation   trees searched  
RAS α 0.50 0.50 -4245.78 698 17 min
Tuffley-Steel s01 1.875 1.66 -4752.23 648 14 min
  s10 1.25 0.80    
Galtier α 0.5 0.41 -4188.25 673 6 hr 52 min
  s11 1.5 2.29    
  π 0.6 0.57    
Huelsenbeck α 0.5 0.46 -4070.79 648 6 hr 8 min
  s01 1.875 1.89    
  s10 1.25 0.83    
General α 0.5 0.50 -4156.24 672 6 hr 26 min
  s01 1.5 1.00    
  s10 2 1.35    
  s11 2.5 5.35    
  π 0.6 0.62