PAL2NAL output

>Q25128
atgaggtctttggtgcttctctgtgttttgctgatggcaatatgtgcggcggacaaaaaa
tccacggtctcgaaggaaaatgcagccgcaatgaaggtagcgatgataaagtttttggat
tcgaggacggatagattcaaaaaacgcattgagaagattggatatccaataacccctccg
caatatacaactctactatactacaacagagagagattgatggattggtgccataactac
gttgaagtatccaaaaagattatattgttgggaggtaacaaattaaataagaagaacttc
gctaggatgggtcgaatcattggctggaaaaaccagtggattttgaaaaggaggcaatgg
cacatggtcagagtgatgaggcgctataaagcttctgcaatagctaaaaagatcgtcgcc
atgaaagttgctgacctaccctgtaac
>Q25012
atgaggtctttggtgcttctctgtgttttgctgatggcaatatgtgcggcggacaaaaaa
acctcggtctcgaaggaaaatgaagccgcaatgaaggtagcgatgatgaagtttttggat
atgaaggcgggtgtattcaaagaaatcattgaggatatgggatatccaataacccctccg
caatggacaactctactgtactacaacagagagagattgattgaattttgccgttccttc
cttgcattgtccaaaaagattatattgctgggaggtaacaaattaaataaggcgaacttc
gctaggatgggtcgaatccttggctggaaaagccagtgggctgtgagacagaggcaatgg
gggatggtcagagtgtcgaggcgccatacaagtactgcaatagctaaaaggatcgtcgcc
atgaaagttgctgacctaccctgtaac
Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
KS = 0.0269
KA = 0.1733
KA/KS = 6.4390
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.