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Table 1 Difference of logarithm likelihood and CPU time when using different α vectors

From: Reconstruction of ancestral protein sequences and its applications

  α = 1.0 α AB α ML
    Δl P*   Δl P*
Logarithm Likelihood -5324.56 -5087.72 236.84 <0.0001 -4987.27 337.29 <0.0001
CPU Time (s)+ 213   213 359
  1. The alignment tested here is a subset of SH2 family. It includes 44 sequences and each sequence contains 83 amino acids (including gaps).
  2. * The likelihood ratio test (LRT) [58] is used to test whether α AB and α ML are significantly different from α = 1.0. The difference in number of free parameters between α AB , α ML and α = 1.0 model is 82.
  3. + CPU times were computed on a Dell PowerEdge 8450 server (CPU 700MHz, RAM 8G).