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I am also confused with the other conclusion of this paper — 'Ka is better than Ka/Ks and Ks for evolutionary estimation'.
As Cribb et al [ 48] pointed it out in detail, however, evolutionary estimation of the character transformation using a parsimony approach does not always produce the best solution and it might be misleading when information utilized for the analysis is incomplete.
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To improve the accuracy of evolutionary distance estimation and ancestral sequence reconstruction, two approaches are proposed to estimate position-specific evolutionary rates.
BEAST is a flexible analysis package for evolutionary parameter estimation and hypothesis testing.
Consideration of rate variation among sites not only improves evolutionary distance estimation, but also gives more accurate ancestral sequence reconstruction.
Two methods of simulating amino acid substitution process were used to test the reliability of reconstruction, rate factors and evolutionary distance estimation.
Domains shorter than 60 amino acids or with a dN > 0.5 or dS > 2 were discarded to ensure robustness in the evolutionary rate estimation.
To delineate the exact boundaries of the newly identified human exons, pairwise comparisons and evolutionary rate estimation were performed for different functional domains of the gene using OWEN alignments (19).
Because the C. reinhardtii cpDNA is one of the most rearranged chloroplast genomes sequenced to date, we included all available chlorophyte chloroplast genomes for evolutionary distance estimation and ancestral gene order reconstruction.
Some of these can be directly compared to genera of the extant family Sargassaceae, as Cystoseirites (similar to Cystoseira) or Paleohalidrys (which has modern representatives) that are in the order Fucales, and provide a valuable framework for evolutionary parameter estimation and molecular dating of Fucaceae [ 37].
After the evolutionary parameter estimations were performed with five test cases sequentially, the parameters have been adjusted, and consequently the Equation 6a was specified to Equation 6b.
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