PAL2NAL output


ERROR:  if "codon(Output format)" is selected, don't use "Remove gaps, inframe stop codons" or "Remove mismatches" or "Use only selected positions".






Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:

       
    K_S = 2.5240


       
    K_A = 0.2252


       
    K_A/K_S = 0.0892

You can see the parameters used in codeml to calculate these values.
If you use these values, please cite the following peper:

    
    Goldman, N. and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11:725-736.

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 2.5240
	K_A = 0.2252
	K_A/K_S = 0.0892
You can see the parameters used in codeml to calculate these values.
If you use these values, please cite the following peper:
	Goldman, N. and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11:725-736.