PAL2NAL output

CLUSTAL W multiple sequence alignment

SUCD_ECOLI    atgtccattttaatcgataaaaacaccaaggttatctgccagggctttaccggtagccag
VIBRO_ORT     ATGTCGATTCTTATCAATAAAGACACTAAAGTCATTTGTCAGGGTTTCACCGGTGGTCAA

SUCD_ECOLI    gggactttccactcagaacaggccattgcatacggcactaaaatggttggcggcgtaacc
VIBRO_ORT     GGTACTTTCCACTCTGAACAGGCGATTGCTTATGGCACACAAATGGTTGGTGGTGTATCG

SUCD_ECOLI    ccaggtaaaggcggcaccacccacctcggcctgccggtgttcaacaccgtgcgtgaagcc
VIBRO_ORT     CCAGGTAAAGGCGGTACCACGCATCTAGGTCTACCGGTATTTAATACCGTTCGTGAAGCC

SUCD_ECOLI    gttgctgccactggcgctaccgcttctgttatctacgtaccagcaccgttctgcaaagac
VIBRO_ORT     GTTGAAGTGACTGGCGCAACCGCAACTGTTATCTACGTACCAGCACCATTTTGTAAAGAT

SUCD_ECOLI    tccattctggaagccatcgacgcaggcatcaaactgattatcaccatcactgaaggcatc
VIBRO_ORT     GCGATTCTGGAAGCGATCGATGCTGGCATCAAGCTTATTGTGACCATCACTGAAGGCATT

SUCD_ECOLI    ccgacgctggatatgctgaccgtgaaagtgaagctggatgaagcaggcgttcgtatgatc
VIBRO_ORT     CCTACCACTGACATGATTGATGTCAAAGTGAAACTGGAACAGACTGGCGTTCGTATGATT

SUCD_ECOLI    ggcccgaactgcccaggcgttatcactccgggtgaatgcaaaatcggtatccagcctggt
VIBRO_ORT     GGCCCTAACTGCCCAGGTGTGATTACACCGGATGAGTGTAAGATTGGCATCATGCCAGGA

SUCD_ECOLI    cacattcacaaaccgggtaaagtgggtatcgtttcccgttccggtacactgacctatgaa
VIBRO_ORT     CACATTCACAAGAAAGGTAAAGTGGGTATCGTTTCTCGCTCTGGTACTTTGACTTATGAA

SUCD_ECOLI    gcggttaaacagaccacggattacggtttcggtcagtcgacctgtgtcggtatcggcggt
VIBRO_ORT     GCGGTTAAACAAACCACAGACGAAGGTTTCGGCCAGTCTACCTGTGTGGGCATCGGTGGC

SUCD_ECOLI    gacccgatcccgggctctaactttatcgacattctcgaaatgttcgaaaaagatccgcag
VIBRO_ORT     GACCCAATTCCGGGGTCAAACTTCATCGACATCCTGAAGATGTTCCAAGAAGATCCAGCG

SUCD_ECOLI    accgaagcgatcgtgatgatcggtgagatcggcggtagcgctgaagaagaagcagctgcg
VIBRO_ORT     ACTGAAGCGATTGTGATGATCGGTGAAATCGGCGGTACCGCGGAAGAAGAAGCAGCTGCT

SUCD_ECOLI    tacatcaaagagcacgttaccaagccagttgtgggttacatcgctggtgtgactgcgccg
VIBRO_ORT     TTCATCAAAGCCAACGTCACAAAACCTGTCGTTTCTTATATCGCAGGTGTAACGGCTCCT

SUCD_ECOLI    aaaggcaaacgtatgggccacgcgggtgccatcattgccggtgggaaagggactgcggat
VIBRO_ORT     CCGGGCAAACGCATGGGTCATGCTGGTGCGATCATCTCTGGTGGTAAAGGTACCGCTGAA

SUCD_ECOLI    gagaaattcgctgctctggaagccgcaggcgtgaaaaccgttcgcagcctggcggatatc
VIBRO_ORT     GAGAAATTTGCAGCACTTGAGTCTGCGGGCGTGAAGACAGTAAAAAGTCTTGCCGATATT

SUCD_ECOLI    ggtgaagcactgaaaactgttctgaaa
VIBRO_ORT     GGCAAAGCGCTGCGTGAAGTGACTGGC

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 46.3501
	K_A = 0.0867
	K_A/K_S = 0.0019
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.