PAL2NAL output

CLUSTAL W multiple sequence alignment

ASPG2_ECOLI    atggagtttttcaaaaagacggcacttgccgcactggttatgggttttagtggtgcagca
CAL11614       atgaaatctataaagctaactgtcttagccggaatcttagcagggatcagcggttcggcc

ASPG2_ECOLI    ttggcattacccaatatcaccattttagcaaccggcgggaccattgccggtggtggtgac
CAL11614       tttgctctgcccaatattaccttattggcgaccgggggaactattgccggtggcggtgat

ASPG2_ECOLI    tccgcaaccaaatctaactacacagtgggtaaagttggcgtagaaaatctggttaatgcg
CAL11614       tcagccactaaatctaactatactgcgggcaaactaggggtcgatgctctggttaacgct

ASPG2_ECOLI    gtgccgcaactaaaagacattgcgaacgttaaaggcgagcaggtagtgaatatcggctcc
CAL11614       gtgccagaaatgaaaaaactcgccaatattcagggtgagcaagtggtcaatatcggttct

ASPG2_ECOLI    caggacatgaacgataatgtctggctgacactggcgaaaaaaattaacaccgactgcgat
CAL11614       caggatatgaatgatgaagtttggctgaaattagcgaaaaaaattaatgctgattgtgcc

ASPG2_ECOLI    aagaccgacggcttcgtcattacccacggtaccgacacgatggaagaaactgcttacttc
CAL11614       aaaaccgacggattcgtcatcactcatgggactgatacattggaggaaactgcctatttc

ASPG2_ECOLI    ctcgacctgacggtgaaatgcgacaaaccggtggtgatggtcggcgcaatgcgtccgtcc
CAL11614       ctcgatttaactgtcaattgtgataagcctgtggtgatggttggggcaatgcgcccggcc

ASPG2_ECOLI    acgtctatgagcgcagacggtccattcaacctgtataacgcggtagtgaccgcagctgat
CAL11614       accgctctgggggcagacggtccgcttaatctctacaacgccgtggtggttgccagtgac

ASPG2_ECOLI    aaagcctccgccaaccgtggcgtgctggtagtgatgaatgacaccgtgcttgatggccgt
CAL11614       cctaactccgctaaacgcggcgtgctggtggcgatgaatgatacggtgttaaccggccgt

ASPG2_ECOLI    gacgtcaccaaaaccaacaccaccgacgtagcgaccttcaagtctgttaactacggtcct
CAL11614       gatgtcatgaaaaccaacaccacttcggtgcaaactttccaatcacctaatactggccct

ASPG2_ECOLI    ctgggttacattcacaacggtaagattgactaccagcgtaccccggcacgtaagcatacc
CAL11614       ctgggctatatctatgatggtaaagtgaactatcttcatcagcctgcaccacgccagcca

ASPG2_ECOLI    ccattcgatgtctctaagctgaatgaactgccgaaagtcggcattgtttataactacgct
CAL11614       gcctttgatatcagcaagctaaatgagttaccgaaagtgggtattatttataactatgcc

ASPG2_ECOLI    aacgcatccgatcttccggctaaagcactggtagatgcgggctatgatggcatcgttagc
CAL11614       aatgcctctgacttacccgctaaggcattgattgaagatggttataaaggaattgtcagt

ASPG2_ECOLI    gctggtgtgggtaacggcaacctgtataaatctgtgttcgacacgctggcgaccgccgcg
CAL11614       gccggtgtgggtaacggtaacctgtataaaacagtattcgatacgttggcaactgcggca

ASPG2_ECOLI    aaaaccggtactgcagtcgtgcgttcttcccgcgtaccgacgggcgctaccactcaggat
CAL11614       cacaatggcgtcgcggtagtgcgttcatcccgtgtccccactggctctaccaccgaagat

ASPG2_ECOLI    gccgaagtggatgatgcgaaatacggcttcgtcgcctctggcacgctgaacccgcaaaaa
CAL11614       gctgaagtggatgataccaaatatggctttgttgcttctggctcacttaatccacaaaaa

ASPG2_ECOLI    gcgcgcgttctgctgcaactggctctgacgcaaaccaaagatccgcagcagatccagcag
CAL11614       gcacgggtactgctgcaattggcattaacccaaacgcaaaaaccgcaagaaattcaaaag

ASPG2_ECOLI    atcttcaatcagtac
CAL11614       ttgttccacgcgtat

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 11.8702
	K_A = 0.1530
	K_A/K_S = 0.0129
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.