PAL2NAL output

>P75691|YAHK_ECOLI
atgaagatcaaagctgttggtgcatattccgctaaacaaccacttgaaccgatggatatc
acccggcgtgaaccgggaccgaatgatgtcaaaatcgaaatcgcttactgtggcgtttgc
cattccgatctccaccaggtccgttccgagtgggcggggacggtttacccctgcgtgccg
ggtcatgaaattgtggggcgtgtggtagccgttggtgatcaggtagaaaaatatgcgccg
ggcgatctggtcggtgtcggctgcattgtcgacagttgtaaacattgcgaagagtgtgaa
gacgggttggaaaactactgtgatcacatgaccggcacctataactcgccgacgccggac
gaaccgggccatactctgggcggctactcacaacagatcgtcgttcatgagcgatatgtt
ctgcgtattcgtcacccgcaagagcagctggcggcggtggctcctttgttgtgtgcaggg
atcaccacgtattcgccgctacgtcactggcaggccgggccgggtaaaaaagtgggcgtg
gtcggcatcggcggtctgggacatatggggattaagctggcccacgcgatgggggcacat
gtggtggcatttaccacttctgaggcaaaacgcgaagcggcaaaagccctgggggccgat
gaagttgttaactcacgcaatgccgatgagatggcggctcatctgaagagtttcgatttc
attttgaatacagtagctgcgccacataatctcgacgattttaccaccttgctgaagcgt
gatggcaccatgacgctggttggtgcgcctgcgacaccgcataaatcgccggaagttttc
aacctgatcatgaaacgccgtgcgatagccggttctatgattggcggcattccagaaact
caggagatgctcgatttttgcgccgaacatggcatcgtggctgatatagagatgattcgg
gccgatcaaattaatgaagcctatgagcgaatgctgcgcggtgatgtgaaatatcgtttt
gttatcgataatcgcacactaacagac
>Q4ZTQ2|Q4ZTQ2_PSEU2
atgctgtcgtacggcgttacacttatccccattgaacaggtgacagtaatggtcaagaca
tacagctacgcagcgcaatcggctcaggacacactcaagccccatcaattcgaacgttgc
tcgcccggcgctgacgatgttcagatcgacatcctttactgcggcgtgtgccactccgat
ctgcatactgcgcgcaatgagtggcacaacacactctatccttctgttccgggtcacgaa
atcgtcggccgggtcacggcggtcggctccgacgtcaagcaattcaaggtaggcgacctg
gctggcgtcggttgcatggtcgacagttgccagcaatgtgcatcgtgcgccgaaggtgac
gagcaatactgcgagagcggcttcaccggcacctacaatggaccggtatttggcggcgag
aacacattcggcggctactccgacaagatcgtggtcaaggaaaagttcgtcttgcgcatc
tcacatgatgccaacctggccgccgtcgcgccgctgttgtgcgcaggtatcaccacctat
tcccccttgcgccactggaaggtcggccccggcaagaaagtcggcattgtcgggcttggc
ggcctcggccacatgggcgtcaagatcgcccacgccatgggcgcccatgtggtgctgttc
acgacctcccccgacaagcgcgaagatggcttgcgtctgggcgccgacgaagtggtcgta
tccagggacgcgggacagatggccgcgcaggccaacagcctggactttatcctcaacacg
gtcgcagcgccgcatgacctggacgccttcctgtctcttctcaagcgcgacggcaccatg
acactggttggcgcgccggcagaaccgcatccgtcacccgcagtgttcaacctgatcttc
aagcgtcgcagcctggccggctcgttgatcggaggcattcaggaaacccaggaaatgctg
gacttctgcgccgagcacggcatcgtttccgacattgaagtgatcgccatgcaggacatc
aacgaggcttacgagcggatgctcaag
Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
KS = 37.0911
KA = 4.2451
KA/KS = 0.1145
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.