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 (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package: 
 KS = 2.2360 
 KA = 0.2265 
 KA/KS = 0.1013 
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. 
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©Пономарева Ольга