PAL2NAL output

CLUSTAL W multiple sequence alignment

DEOC_ECOLI    atgactgatctgaaagcaagcagcctgcgtgcactgaaattgatggacctgaccaccctg
DEOC_PHOLL    atgaccgatttaaccgcagcagcgcagcgtgcgctgagtttgatggatttaacgacactc

DEOC_ECOLI    aatgacgacgacaccgacgagaaagtgatcgccctgtgtcatcaggccaaaactccggtc
DEOC_PHOLL    aatgataatgataccgatgaaaaagtgacggcactttgtcatcaggcgaaaagcctcgcg

DEOC_ECOLI    ggcaataccgccgctatctgtatctatcctcgctttatcccgattgctcgcaaaactctg
DEOC_PHOLL    ggcaatactgcggctatctgtatctaccctcgttttattcctctggcacgtaaagtatta

DEOC_ECOLI    aaagagcagggcaccccggaaatccgtatcgctacggtaaccaacttcccacacggtaac
DEOC_PHOLL    cgtgaacagggcacacctgaaatccgcattgcaacagtgacaaacttcccacatggtcat

DEOC_ECOLI    gacgacatcgacatcgcgctggcagaaacccgtgcggcaatcgcctacggtgctgatgaa
DEOC_PHOLL    gacgatattgacatcgctttagctgaaacccaagcggctattgcttatggcgctgatgag

DEOC_ECOLI    gttgacgttgtgttcccgtaccgcgcgctgatggcgggtaacgagcaggttggttttgac
DEOC_PHOLL    gtcgatgtggttttcccataccgtgcattgatggccagtaatgaacaagtcggttttgag

DEOC_ECOLI    ctggtgaaagcctgtaaagaggcttgcgcggcagcgaatgtactgctgaaagtgatcatc
DEOC_PHOLL    atggtaaaagcgtgtaaagtcgcctgtgcagaagcggatgtgctgctaaaagttattatt

DEOC_ECOLI    gaaaccggcgaactgaaagacgaagcgctgatccgtaaagcgtctgaaatctccatcaaa
DEOC_PHOLL    gaaactggtgaactgaaagaggcatctctgatccgtaaggcatctgaaatttcaatcaac

DEOC_ECOLI    gcgggtgcggacttcatcaaaacctctaccggtaaagtggctgtgaacgcgacgccggaa
DEOC_PHOLL    gcgggtgccgattttatcaaaacatctacaggtaaagtgccggttaacgcgacattggca

DEOC_ECOLI    agcgcgcgcatcatgatggaagtgatccgtgatatgggcgtagaaaaaaccgttggtttc
DEOC_PHOLL    agtgctgaaatcatgatgaaggtgattcatgagatgggcgtgggtgaaacggttggcttc

DEOC_ECOLI    aaaccggcgggcggcgtgcgtactgcggaagatgcgcagaaatatctcgccattgcagat
DEOC_PHOLL    aaaccggctggtggcgtgcgtaccgctgaagaggctgcacaatatctggcattagctgat

DEOC_ECOLI    gaactgttcggtgctgactgggcagatgcgcgtcactaccgctttggcgcttccagcctg
DEOC_PHOLL    catatcatgggtgacaaatgggttgatgcccgtcattttcgttttggggcttctagcttg

DEOC_ECOLI    ctggcaagcctgctgaaagcgctgggtcacggcgacggtaagagcgccagcagctac
DEOC_PHOLL    ttaggcaatttgctaaatactctgggtcatcaggggcaaaaacaaagcagccattat

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 2.6956
	K_A = 0.1418
	K_A/K_S = 0.0526
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.