PAL2NAL output

CLUSTAL W multiple sequence alignment

Q25153_HALSO    atgaggtctttggtgcttctctgtgttttgctgatggcaatatgtgcggcggacaaaaaa
Q25012_9VEST    atgaggtctttggtgcttctctgtgttttgctgatggcaatatgtgcggcggacaaaaaa

Q25153_HALSO    accacggtctcgaaggaaaatgcagccgcaatgaagatagctatgataaagtttttggat
Q25012_9VEST    acctcggtctcgaaggaaaatgaagccgcaatgaaggtagcgatgatgaagtttttggat

Q25153_HALSO    gcgagggcgggtaaattcaaaaaacgcgttgagaatatgggatatccaataacccctccg
Q25012_9VEST    atgaaggcgggtgtattcaaagaaatcattgaggatatgggatatccaataacccctccg

Q25153_HALSO    caatggacaactctactatactacaacagacagagattgatggaatggtgccatacctac
Q25012_9VEST    caatggacaactctactgtactacaacagagagagattgattgaattttgccgttccttc

Q25153_HALSO    gttgaattttccaaaaagattatattgatgggaggtaacaaattaaataagaagaacttc
Q25012_9VEST    cttgcattgtccaaaaagattatattgctgggaggtaacaaattaaataaggcgaacttc

Q25153_HALSO    actaggatgggtcgaatcattggctggaaaaaccagtgggttttgaaaaggaggcaatgg
Q25012_9VEST    gctaggatgggtcgaatccttggctggaaaagccagtgggctgtgagacagaggcaatgg

Q25153_HALSO    gagatggtcagagtgatgaggcgctataaaagtactgcaatagctaaaaagatcgtcgcc
Q25012_9VEST    gggatggtcagagtgtcgaggcgccatacaagtactgcaatagctaaaaggatcgtcgcc

Q25153_HALSO    atgaaagttgctgacctaccctgtaac
Q25012_9VEST    atgaaagttgctgacctaccctgtaac

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 0.0204
	K_A = 0.1350
	K_A/K_S = 6.6327
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.