PAL2NAL output

CLUSTAL W multiple sequence alignment

BIOD_SALTY    gtgactaaacgctattttgtgaccggtactgatactgaagtcggtaaaacggtcgccagt
BIOD_ECOLI    gtgagtaaacgttattttgtcaccggaacggataccgaagtggggaaaactgtcgccagt

BIOD_SALTY    tgcgccttattgcaggccgcaacgcagttaggttatcaaaccgtaggctataagcccgtc
BIOD_ECOLI    tgtgcacttttacaagccgcaaaggcagcaggctaccggacggcaggttataaaccggtc

BIOD_SALTY    gcttccggcagcgaaatgacaaccgacgggctacgcaatagcgatgccctggccttgcag
BIOD_ECOLI    gcctctggcagcgaaaagaccccggaaggtttacgcaatagcgacgcgctggcgttacag

BIOD_SALTY    cgtaacagcagcctgccgcaaccttattccgctatcaatccttatacttttgccgagcct
BIOD_ECOLI    cgcaacagcagcctgcagctggattacgcaacagtaaatccttacaccttcgcagaaccc

BIOD_SALTY    acctctccccacatcgttagcgccgacgaaggccgggcgatagacgcggcggtgttatca
BIOD_ECOLI    acttcgccgcacatcatcagcgcgcaagagggcagaccgatagaatcattggtaatgagc

BIOD_SALTY    cgcggattgcgaacgctggaggcgcaggcagactgggtgttgacagaaggggcgggcggc
BIOD_ECOLI    gccggattacgcgcgcttgaacaacaggctgactgggtgttagtggaaggtgctggcggc

BIOD_SALTY    tggtttacaccgctctctgccacgctgacgtttgccgactgggtacagacggagcagctg
BIOD_ECOLI    tggtttacgccgctttctgacactttcacttttgcagattgggtaacacaggaacaactg

BIOD_SALTY    ccggtgattctggttgttggcgtcaagctgggctgtattaatcacgccatgctgacggcg
BIOD_ECOLI    ccggtgatactggtagttggtgtgaaactcggctgtattaatcacgcgatgttgactgca

BIOD_SALTY    ctggcggtagaacaggccggattaccgcttgtcggatggatagccaacgacatacagccg
BIOD_ECOLI    caggtaatacaacacgccggactgactctggcgggttgggtggcgaacgatgttacgcct

BIOD_SALTY    ccaggcgcgcgtcatggtgaatatctcgcgacgcttcgccgcgtcataccggccccgcta
BIOD_ECOLI    ccgggaaaacgtcacgctgaatatatgaccacgctcacccgcatgattcccgcgccgctg

BIOD_SALTY    ttaggggaaatcccgtggctgggcgtttctccatcgcaggcggcgacaggacagtatctg
BIOD_ECOLI    ctgggagagatcccctggcttgcagaaaatccagaaaatgcggcaaccggaaagtacata

BIOD_SALTY    gaccttagccccctg
BIOD_ECOLI    aaccttgccttgttg

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 1.7932
	K_A = 0.1829
	K_A/K_S = 0.1020
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.