PAL2NAL output

CLUSTAL W multiple sequence alignment

BIOB_ECOLI    caccgcccacgctggacattgtcgcaagtcacagaattatttgaaaaaccgttgctggat
BIOB_BUCAP    atgaaacgaaaatggaacctagaagatacaaaaaaacttttttcaaaacccttttttgat

BIOB_ECOLI    ctgctgtttgaagcgcagcaggtgcatcgccagcatttcgatcctcgtcaggtgcaggtc
BIOB_BUCAP    cttatattcgaagctcaaaaaaaacaccgtgaatattttaatcctaatagaatacaaatt

BIOB_ECOLI    agcacgttgctgtcgattaagaccggagcttgtccggaagattgcaaatactgcccgcaa
BIOB_BUCAP    agtacattactatcaattaaaactggagcgtgtccagaagattgcaagtattgtccacaa

BIOB_ECOLI    agctcgcgctacaaaaccgggctggaagccgagcggttgatggaagttgaacaggtgctg
BIOB_BUCAP    agttcaagatataaaactggtttaaaaaaagagccgttattagaaatagaacaaatttta

BIOB_ECOLI    gagtcggcgcgcaaagcgaaagcggcaggatcgacgcgcttctgtatgggcgcggcgtgg
BIOB_BUCAP    aaagctgcaaaaaaagctaaatcttcaggttcaactcgattttgcatgggtgctgcatgg

BIOB_ECOLI    aagaatccccacgaacgcgatatgccgtacctggaacaaatggtgcagggggtaaaagcg
BIOB_BUCAP    aaaaatcctaaagaaaaagatatgccatatttagaaaaaattgttaaagaagtaaaaaaa

BIOB_ECOLI    atggggctggaggcgtgtatgacgctgggcacgttgagtgaatctcaggcgcagcgcctc
BIOB_BUCAP    atgggcatggaaacctgtatgactttaggaacattaaataattctcaggcaaaaaaatta

BIOB_ECOLI    gcgaacgccgggctggattactacaaccacaacctggacacctcgccggagttttacggc
BIOB_BUCAP    gctaaagcaggtttagatttttataatcataatttagatacatcatctaatttttatagc

BIOB_ECOLI    aatatcatcaccacacgcacttatcaggaacgcctcgatacgctggaaaaagtgcgcgat
BIOB_BUCAP    agtattataacaactcgtacatatgaagaacgtttaagtactttaaaaaaggttcgaaat

BIOB_ECOLI    gccgggatcaaagtctgttctggcggcattgtgggcttaggcgaaacggtaaaagatcgc
BIOB_BUCAP    tcaggtatgaaaatttgttctggaggaattattggtcttggggaaaaaaaacaagatcgt

BIOB_ECOLI    gccggattattgctgcaactggcaaacctgccgacgccgccggaaagcgtgccaatcaac
BIOB_BUCAP    atggaacttttaatggaattatctaatttatctattcaaccagaaagtgtaccaataaat

BIOB_ECOLI    atgctggtgaaggtgaaaggcacgccgcttgccgataacgatgatgtcgatgcctttgat
BIOB_BUCAP    atgttagtaaaaataccaggaacacctatggaaaaaaatgaaaatgtcgatccatttgaa

BIOB_ECOLI    tttattcgcaccattgcggtcgcgcggatcatgatgccaacctcttacgtgcgcctttct
BIOB_BUCAP    tttattagagttattgcagctacaagaattatgatgccaaaatcttatattcgattgtct

BIOB_ECOLI    gccggacgcgagcagatgaacgaacagactcaggcgatgtgctttatggcaggcgcaaac
BIOB_BUCAP    gcaggtcgtgaaaacatgagtgatgaaactcaagctatgtgttttatggcaggagcaaat

BIOB_ECOLI    tcgattttctacggttgcaaactgctgaccacgccgaatccggaagaagataaagacctg
BIOB_BUCAP    tctattttttatggatgtaaattattaacttcaagtaatccgaaagaagaaaaagatcaa

BIOB_ECOLI    caactgttccgcaaactggggctaaatccgcaaactgccgtgctggcaggggataacgaa
BIOB_BUCAP    aaactttttgaaaaattagatctttttcctgattacaagatacaaagcattacagaagaa

BIOB_ECOLI    caacagcaacgtcttgaacaggcgctgatgaccccggacaccgacgaatattacaacgcg
BIOB_BUCAP    aataaaaataatgaaaacttaaaaatatctgatgtaaataaagcacaatactataatgcg

BIOB_ECOLI    gcagca
BIOB_BUCAP    gcaatt

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 51.8874
	K_A = 0.2574
	K_A/K_S = 0.0050
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.