PAL2NAL output

#------------------------------------------------------------------------#
#  WARNING: ILVC_ECOLI pepAlnPos 1: M does not correspond to atg
#  WARNING: ILVC_ECOLI pepAlnPos 251: E does not correspond to aaa
#------------------------------------------------------------------------#

>ILVC_ECOLI
atggctaactacttcaatacactgaatctgcgccagcagctggcacagctgggcaaatgt
cgctttatgggccgcgatgaattcgccgatggcgcgagctaccttcagggtaaaaaagta
gtcatcgtcggctgtggcgcacagggtctgaaccagggcctgaacatgcgtgattctggt
ctcgatatctcctacgctctgcgtaaagaagcgattgccgagaagcgcgcgtcctggcgt
aaagcgaccgaaaatggttttaaagtgggtacttacgaagaactgatcccacaggcggat
ctggtgattaacctgacgccggacaagcagcactctgatgtagtgcgcaccgtacagcca
ctgatgaaagacggcgcggcgctgggctactcgcacggtttcaacatcgtcgaagtgggc
gagcagatccgtaaagatatcaccgtagtgatggttgcgccgaaatgcccaggcaccgaa
gtgcgtgaagagtacaaacgtgggttcggcgtaccgacgctgattgccgttcacccggaa
aacgatccgaaaggcgaaggcatggcgattgccaaagcctgggcggctgcaaccggtggt
caccgtgcgggtgtgctggaatcgtccttcgttgcggaagtgaaatctgacctgatgggc
gagcaaaccatcctgtgcggtatgttgcaggctggctctctgctgtgcttcgacaagctg
gtggaagaaggtaccgatccagcatacgcgaaaaaactgattcagttcggttgggaaacc
atcaccgaagcactgaaacagggcggcatcaccctgatgatggaccgtctctctaacccg
gcgaaactgcgtgcttatgcgctttctgaacagctgaaagagatcatggcacccctgttc
cagaaacatatggacgacatcatctccggcgaattctcttccggtatgatggcggactgg
gccaacgatgataagaaactgctgacctggcgtgaagagaccggcaaaaccgcgtttgaa
accgcgccgcagtatgaaggcaaaatcggcgagcaggagtacttcgataaaggcgtactg
atgattgcgatggtgaaagcgggcgttgaactggcgttcgaaaccatggtcgattccggc
atcattgaagagtctgcatattatgaatcactgcacgagctgccgctgattgccaacacc
atcgcccgtaagcgtctgtacgaaatgaacgtggttatctctgataccgctgagtacggt
aactatctgttctcttacgcttgtgtgccgttgctgaaaccgtttatggcagagctgcaa
ccgggcgacctgggtaaagctattccggaaggcgcggtagataacgggcaactgcgtgat
gtgaacgaagcgattcgcagccatgcgattgagcaggtaggtaagaaactgcgcggctat
atgacagatatgaaacgtattgctgttgcgggt
>ILVC_YERPA
atggctaactatttcaacacattgaacctgcgtcagcagttggcgcaattaggtaagtgt
cgctttatggcacgtgacgaatttgccgatgaagccggctacctgaaaggcaaaaaagtg
gtgattgtcggttgtggcgcacagggcctgaaccaagggttgaacatgcgtgactccggc
ctggatgtcgcttatgccctgcgtaaagaagcgattgccgagaagcgtgcttcatggcgt
aaagcgaccgaaaatggtttcaaagtaggcacttacgaagagttgatcccacaggcggat
ctggtggttaacctgacgccagacaagcagcactctgccgtggttaaggcggttcagcct
ctgatgaaagagggcgcagcactgggttactcgcatggtttcaacattgttgaagtgggt
gagcaagtgcgtaaagacatcaccgtggtgatggttgcgccgaaatgccctggtaccgaa
gttcgtgaagagtacaaacgtggttttggtgtgccgacgctgattgcggttcatccagaa
aacgaccctaaaggcgaaggcatggcgattgctaaagcctgggccgcggccaccggtggt
caccgtgcgggtgtactggaattttcttttgttgccgaagtgaaatctgacctgatgggc
gagcaaactatcctgtgtggtatgttgcaggcgggttcactgttatgtttcgacaagttg
gtttcagagggtactgatgccgcttacgctgaaaaactgattcaattcggctgggaaacc
attaccgaagcgctgaaacaaggcgggatcacgctgatgatggaccgtttgtctaatcca
gcaaaactgcgtgcgtatgcattatctgaacagttgaaagaaattatggcgccattgttc
cagaaacacatggacgacattatttctggtgcgttctccagcggcatgatggctgactgg
gctaacgatgacgttaagttgttgaactggcgtgaagagaccggcagaacggcttttgaa
aatgcgccacagtttgaaggcaagatctctgagcaggaatattttgaccacggcgtactg
atgatcgcgatggtaaaagcgggagttgagctggcattcgaaaccatggtggattccggc
attattgaagagtctgcttactacgaatctctgcacgagctgccgttgattgccaacact
atcgcccgtaagcgtctgtatgaaatgaacgtggttatctctgataccgcagaatacggt
aactacttgtttgctaatgcagcggtgccgttgctgaaagagtttatggattccctgcaa
gccggtgacttgggtaaaagtatccctggttcggcggtagataacgcacaactgcgtgat
gtgaatgaagccattcgcaatcacccgatcgaagccgttggtcataagctgcgtggttac
atgacagatatgaagcgtattgctgttgcgggc


Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
KS = 0.8467
KA = 0.0516
KA/KS = 0.0610
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.