PAL2NAL output

CLUSTAL W multiple sequence alignment

MODE_ECOLI    atgcaggccgaaatccttctcacccttaagctccaacaaaaattattcgccgacccgcgc
MODE_YERPE    atgcaggccgaaattcttcttacactaaaacttcaacagcgcctgtttgccgatccacgc

MODE_ECOLI    cgcatttcgctactaaaacacattgcgctttccggttccattagccagggagcgaaagat
MODE_YERPE    cgtattgcactgttaaagcaaattcagcataccggttccatcagccagggagccaagctc

MODE_ECOLI    gccggtattagctataaaagcgcctgggatgccattaacgagatgaatcagttaagtgag
MODE_YERPE    gcgggtatcagctataaaagtgcctgggatgccataaatgacatgaatacactgtccgag

MODE_ECOLI    catattctggtcgagcgcgcaacaggcggtaaaggtggcggcggcgcagtactgacccgc
MODE_YERPE    gagatactggttgaacgggccactggcggcaaaggtggagggggtgcacatctgacccgc

MODE_ECOLI    tatggtcagcgactgattcagctctatgacttactggcgcaaatccagcaaaaagccttt
MODE_YERPE    tacggtgaacgcttaatccagctttatgatttactcgcaaccatccagcaaaaagccttt

MODE_ECOLI    gatgtgttaagtgatgacgccctgccgctgaacagcctgctggccgcgatctcacgtttt
MODE_YERPE    gataccctgaaagatgattcactgccgctggacagcttgctggcggcaatttcccgtttt

MODE_ECOLI    tcactgcaaaccagcgcccgtaaccagtggttcggtaccatcaccgcccgcgatcatgat
MODE_YERPE    tcactgcaaaccagcgcccgtaatcaatttttcggtacccttattgaacgcgaccaccag

MODE_ECOLI    gacgttcaacagcatgttgatgtcttactggctgacggaaaaacacgcctgaaagtcgca
MODE_YERPE    caggtgcaacagcatgtcaatattctgctatcggacggtaaaactcgcttaacggcggcg

MODE_ECOLI    attaccgcacaaagcggcgcgcgtctggggctggatgaaggcaaagaagtgttgatattg
MODE_YERPE    atcacccaacaaagcgcggatcgcctgcaactttcagcaggtaaagaagtgctggcattg

MODE_ECOLI    ctaaaagcgccgtgggtaggtattactcaggacgaggcggtcgcgcaaaacgctgacaac
MODE_YERPE    attaaagcaccttgggtaaaactggttaccgatccggcactggcaggtgcagcggataac

MODE_ECOLI    caattaccgggtattattagtcatattgagcgcggcgcagagcagtgcgaagtattaatg
MODE_YERPE    gcattgccgggaacggtcgccagcattgagccgggcaacgatcatagcgaagttattgtc

MODE_ECOLI    gcgctacccgacgggcaaacactgtgcgccacagtgccggtaaatgaagcgacttctctt
MODE_YERPE    accttaactggcggggccaacctgtgttcaacccaaaacaacagcgaagcgctgaattta

MODE_ECOLI    cagcaaggacagaatgtcacggcctactttaatgccgacagcgtgattatcgccacgctg
MODE_YERPE    cgggttggcagtgccgtcattgcacaattcaatgcagatcgggtgattatcgccacattg

MODE_ECOLI    tgc
MODE_YERPE    tgt

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 1.8925
	K_A = 0.2417
	K_A/K_S = 0.1277
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.