PAL2NAL output

>PABB,
atgaagacgttatctcccgctgtgattactttactctggcgtcaggacgccgctgaattt
tatttctcccgcttaagccacctgccgtgggcgatgcttttacactccggctatgccgat
catccgtatagccgctttgatattgtggtcgccgagccgatttgcactttaaccactttc
ggtaaagaaaccgttgttagtgaaagcgaaaaacgcacaacgaccactgatgacccgcta
caggtgctccagcaggtgctggatcgcgcagacattcgcccaacgcataacgaagatttg
ccatttcagggcggcgcactggggttgtttggctacgatctgggccgccgttttgagtca
ctgccagaaattgcggaacaagatatcgttctgccggatatggcagtgggtatctacgat
tgggcgctcattgtcgaccaccagcgtcatacagtttctttgctgagtcataatgatgtc
aatgcccgtcgggcctggctggaaagccagcaattctcgccgcaggaagatttcacgctc
acttccgactggcaatccaatatgacccgcgagcagtacggcgaaaaatttcgccaggta
caggaatatctgcacagcggtgattgctatcaggtgaatctcgcccaacgttttcatgcg
acctattctggcgatgaatggcaggcattccttcagcttaatcaggccaaccgcgcgcca
tttagcgcttttttacgtcttgaacagggtgcaattttaagcctttcgccagagcggttt
attctttgtgataatagtgaaatccagacccgcccgattaaaggcacgctaccacgcctg
cccgatcctcaggaagatagcaaacaagcagtaaaactggcgaactcagcgaaagatcgt
gccgaaaatctgatgattgtcgatttaatgcgtaatgatatcggtcgtgttgccgtagca
ggttcggtaaaagtaccagagctgttcgtggtggaacccttccctgccgtgcatcatctg
gtcagcaccataacggcgcaactaccagaacagttacacgccagcgatctgctgcgcgca
gcttttcctggtggctcaataaccggggctccgaaagtacgggctatggaaattatcgac
gaactggaaccgcagcgacgcaatgcctggtgcggcagcattggctatttgagcttttgc
ggcaacatggataccagtattactatccgcacgctgactgccattaacggacaaattttc
tgctctgcgggcggtggaattgtcgccgatagccaggaagaagcggaatatcaggaaact
tttgataaagttaatcgtatcctgaagcaactggagaag
>PABB_SALTY
atgaagacgttatctcccactgttatcaccttaccctggcgtccggacgccgctgaacac
tattttgcgcccgtaaaccatttgccctgggcgatgctgctgcattcaggtgatgctatt
catccctataaccgttttgatattctggtcgccgatcctgtcaccacactgaccacgcgc
gcgcaggaaaccacggtatgtactgcgcgcacgactaccgtcactctcgacgatccgtta
cacgttttgcagactcaactggaggcgctgccttttcatcctcagcctgaccctgactta
ccctttcagggcggcgcgctgggtctgtttggttatgatttagggcggcgtttcgaaatt
ttgcccgatactgccgcgcgcgatatcgctttacccgatatggcgattggcctttacgac
tgggcgctgattgtcgatcaccaaaaacaggtggtgtcgctgataagctatcacgatgca
gacgcccgatatcgctggctcaccagccagcgcgcgccgacccgcacgcccttcaggctt
acctcagcctggcaatccaatatgacgcgttgcgagtatggcgagaagtttcgtcaggtg
caggcctggctgcacagcggggactgctatcaggtcaatctttcccagcgttttcaggcg
agctacgagggtgatgaatggcaggctttcgaacgccttaaccgcgccaatcgcgccccg
ttcagcgcctttcttcgtttacatgacggcgccatattgagcctttctcccgagcgtttt
atccaactggagaatggtcatatccagacgcgcccgatcaaaggtacgcttccacggctt
aacgatccgcaggcggatcgtcagcaggcgcagaaactggctaattcaatgaaagatcgc
gctgaaaatttgatgattgtcgatttgatgcgtaacgatattggccgggtcgccgtacca
ggttcggtgaaagtgccggaactgttcgtcgtcgaaccatttcctgccgttcaccatctg
gttagcaccattaccgcccgtttaccggactcgcttcatgctaccgacctgctgcgcgcg
gctttccccggcggctccattaccggcgcgcctaaagtgcgggcaatggaaattatcgac
gaactggagccgcagcgacgcaacgcctggtgcggtagcatcggttatctgagtttctgc
ggcaagatggataccagtattactatccgcaccgtcacggcaacgcagggccaactctat
tgctcagccggcggcggtatcgtggccgatagcaacgaagaagcggaatatcaggaaact
tttgataaagttaatcgtatcctgcacccactggagaac


Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
KS = 1.5359
KA = 0.1705
KA/KS = 0.1110
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.