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Table 2 Difference of logarithm likelihood and CPU time with and without optimization of π vector

From: Reconstruction of ancestral protein sequences and its applications

  α AB & Calculated π α AB & Optimized π Δl P*
Logarithm Likelihood -5087.72 -5055.97 31.75 <0.0001
CPU Time (s)+ 213 14902   
  1. The alignment tested here is the same alignment used in Table 1. Calculated π means frequency vector calculated from the alignment.
  2. * The likelihood ratio test (LRT) [58] is used to test whether optimized π is significantly different from calculated π. The difference in number of free parameters between these two models is 19.
  3. +CPU times were computed on a Dell PowerEdge 8450 server (CPU 700MHz, RAM 8G).