PAL2NAL output

CLUSTAL W multiple sequence alignment

Q25012        atgaggtctttggtgcttctctgtgttttgctgatggcaatatgtgcggcggacaaaaaa
Q25063        atgaggtctttggtgcttctctgtgttttgatggcggtaggatgtgtggcgtttgatgat

Q25012        acctcggtctcgaaggaaaatgaagccgcaatgaaggtagcgatgatgaagtttttggat
Q25063        gtggtggtctcaaggcaagagcaatcttatgtgcagagagggatggtcaactttttggat

Q25012        atgaaggcgggtgtattcaaagaaatcattgaggatatgggatatccaataacccctccg
Q25063        gaagaaatgcataaactggttaaacggtttagagatatgcgatggaatttagggccaggc

Q25012        caatggacaactctactgtactacaacagagagagattgattgaattttgccgttccttc
Q25063        tttgtattccttctaaaaaaagtcaacagagagagaatgatgcgctactgcatggattac

Q25012        cttgcattgtccaaaaagattatattgctgggaggtaacaaattaaataaggcgaacttc
Q25063        gccagatattccaaaaagattttacagctaaaacatcttccagtaaataagaagaccctc

Q25012        gctaggatgggtcgaatccttggctggaaaagccagtgggctgtgagacagaggcaatgg
Q25063        actaaaatgggtagattcgttggatatcgaaactatggggtcatcagggagttgtacgcc

Q25012        gggatggtcagagtgtcgaggcgccatacaagtactgcaatagctaaaaggatcgtcgcc
Q25063        gacgtattcagagacgttcaaggatttagggggactgcagccatgaggaagtacagcagc

Q25012        atgaaagttgctgacctaccctgtaac
Q25063        aaggatcctggtacatttccttgcaag

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 0.5509
	K_A = 0.9761
	K_A/K_S = 1.7719
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.