PAL2NAL output

CLUSTAL W multiple sequence alignment

AAC37229.1    ATGAGGTCTTTGGTGCTTCTCTGTGTTTTGCTGATGGCAATATGTGCGGCGGACAAAAAA
AAC37231.1    ATGAGGTCTTTGGTGCTTCTCTGTGTTTTGCTGATGGCAATATGTGCGGCGGACAAAAAA

AAC37229.1    TCCACGGTCTCGAAGGAAAATGCAGCCGCAATGAAGGTAGCGATGATAAAGTTTTTGGAT
AAC37231.1    ACCTCGGTCTCGAAGGAAAATGAAGCCGCAATGAAGGTAGCGATGATGAAGTTTTTGGAT

AAC37229.1    TCGAGGACGGATAGATTCAAAAAACGCATTGAGAAGATTGGATATCCAATAACCCCTCCG
AAC37231.1    ATGAAGGCGGGTGTATTCAAAGAAATCATTGAGGATATGGGATATCCAATAACCCCTCCG

AAC37229.1    CAATATACAACTCTACTATACTACAACAGAGAGAGATTGATGGATTGGTGCCATAACTAC
AAC37231.1    CAATGGACAACTCTACTGTACTACAACAGAGAGAGATTGATTGAATTTTGCCGTTCCTTC

AAC37229.1    GTTGAAGTATCCAAAAAGATTATATTGTTGGGAGGTAACAAATTAAATAAGAAGAACTTC
AAC37231.1    CTTGCATTGTCCAAAAAGATTATATTGCTGGGAGGTAACAAATTAAATAAGGCGAACTTC

AAC37229.1    GCTAGGATGGGTCGAATCATTGGCTGGAAAAACCAGTGGATTTTGAAAAGGAGGCAATGG
AAC37231.1    GCTAGGATGGGTCGAATCCTTGGCTGGAAAAGCCAGTGGGCTGTGAGACAGAGGCAATGG

AAC37229.1    CACATGGTCAGAGTGATGAGGCGCTATAAAGCTTCTGCAATAGCTAAAAAGATCGTCGCC
AAC37231.1    GGGATGGTCAGAGTGTCGAGGCGCCATACAAGTACTGCAATAGCTAAAAGGATCGTCGCC

AAC37229.1    ATGAAAGTTGCTGACCTACCCTGTAAC
AAC37231.1    ATGAAAGTTGCTGACCTACCCTGTAAC

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 0.0269
	K_A = 0.1733
	K_A/K_S = 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.