PAL2NAL output

>SYY_ECOLI
ATGGCAAGCAGTAACTTGATTAAACAATTGCAAGAGCGGGGGCTGGTAGCCCAGGTGACG
GACGAGGAAGCGTTAGCAGAGCGACTGGCGCAAGGCCCGATCGCGCTCTATTGCGGCTTC
GATCCTACCGCTGACAGCTTGCATTTGGGGCATCTTGTTCCATTGTTATGCCTGAAACGC
TTCCAGCAGGCGGGCCACAAGCCGGTTGCGCTGGTAGGCGGCGCGACGGGTCTGATTGGC
GACCCGAGCTTCAAAGCTGCCGAGCGTAAGCTGAACACCGAAGAAACTGTTCAGGAGTGG
GTGGACAAAATCCGTAAGCAGGTTGCCCCGTTCCTCGATTTCGACGGAGAAAACTCTGCT
ATCGCGGCGAACAACTATGACTGGTTCGGCAATATGAATGTGCTGACCTTCCTGCGCGAT
ATTGGCAAACACTTCTCCGTTAACCAGATGATCAACAAAGAAGCGGTTAAGCAGCGTCTC
AACCGTGAAGATCAGGGGATTTCGTTCACTGAGTTTTCCTACAACCTGTTGCAGGGTTAT
GACTTCGCCTGTCTGAACAAACAGTACGGTGTGGTGCTGCAAATTGGTGGTTCTGACCAG
TGGGGTAACATCACTTCTGGTATCGACCTGACCCGTCGTCTGCATCAGAATCAGGTGTTT
GGCCTGACCGTTCCGCTGATCACTAAAGCAGATGGCACCAAATTTGGTAAAACTGAAGGC
GGCGCAGTCTGGTTGGATCCGAAGAAAACCAGCCCGTACAAATTCTACCAGTTCTGGATC
AACACTGCGGATGCCGACGTTTACCGCTTCCTGAAGTTCTTCACCTTTATGAGCATTGAA
GAGATCAACGCCCTGGAAGAAGAAGATAAAAACAGCGGTAAAGCACCGCGCGCCCAGTAT
GTACTGGCGGAGCAGGTGACTCGTCTGGTTCACGGTGAAGAAGGTTTACAGGCGGCAAAA
CGTATTACCGAATGCCTGTTCAGCGGTTCTTTGAGTGCGCTGAGTGAAGCGGACTTCGAA
CAGCTGGCGCAGGACGGCGTACCGATGGTTGAGATGGAAAAGGGCGCAGACCTGATGCAG
GCACTGGTCGATTCTGAACTGCAACCTTCCCGTGGTCAGGCACGTAAAACTATCGCCTCC
AATGCCATCACCATTAACGGTGAAAAACAGTCCGATCCTGAATACTTCTTTAAAGAAGAA
GATCGTCTGTTTGGTCGTTTTACCTTACTGCGTCGCGGTAAAAAGAATTACTGTCTGATT
TGCTGGAAA
>SYY_DECAR
ATGTATCAGTCCCCCCTCATCCAGGATCTGCACGATCGCGGCCTGATCGCCCAGATCACC
GACGCTGCGGCGCTCGACAAACTGCTGACTGAGGAATCGGTAACGCTCTATTGCGGCTTC
GACCCGACGGCGGACAGCCTGCACCTCGGCCATCTGGTGCCGGTGCTCATCCTCAAGCGC
TTCCAGGAAGCCGGCCACAAGCCCATCGCGCTGGTTGGCGGCGCCACCGGCATGATCGGC
GACCCGAGTTTCAAGGCCACCGAGCGCAAGCTCAACACGCCGGATGTGATCGCCAGCTGG
GTTGGCAAGATTCGGGGCCAGGTCGAGCCCTTCCTCAAGTTCGACGGCGCCAACGCCGCC
ATCATGGCCAACAACTACGACTGGTTCGGCGGCATGAACTGCCTCGAATTCATGCGCGAC
ATCGGCAAGCATTTCTCGGTCAACGCCATGATCAAGAAGGAATCCGTGCAGCAGCGCCTG
ACCCGCGAAGACCAGGGCATTTCCTACACCGAGTTCTCGTACAGCCTGCTCCAGGGCTAC
GACTTCGCCGAACTCAACAAGCGCTACGGCTGCGTGCTGCAGATCGGCGGCTCCGACCAG
TGGGGCAACATCGTCGCCGGCACCGACCTGACGCGCCGACTGCATCAGAAACATGTCTTC
GGCCTGACCCTGCCGCTGATCACCAAGGCCGACGGCACCAAGTTCGGCAAGACCGAATCC
GGCGCCATCTGGCTCGACCCGAAAAAGACCTCGCCGTACGCCTTCTACCAGTTCTGGCTG
AACACCAGCGACGCCGACGTCTACAAGTTCATGAACTTCTTCACCTTCCTGCCGGTCGCC
CGCATCGCCGAGATCGAAGCGGCCGACAAGGCCAGCGGCACCAAGCCGGAAGCCCAGCGC
ATCCTGGCCGAGGAAGCCACTCGCCTGGTGCACGGCGAAGTCGCGCTGATGGCCGCCCGC
CGCATCACAGAATGCCTGTTCAGCGGCCAGCTCGCCGACCTGACCGAAAACGACCTCGAA
CAACTGGCCCAGGACGGCATGCCCGGCGTGCAGCTGGAATCCAACACCGGTCTGATCGAC
GCCCTTGTTGCAAGCGGTCTGGCCAAGTCGAAATCGGAAGCCCGCACTTTCATCCAGAGC
GGCAGCGTCGCCATCAATGGCAACAAAGCGGAGGCGCTGGACCATGCCATTGGTGGCGAT
GAACTGCTCTACGGCCGTTTCACCATCCTGCGGCGCGGCAAGAAGAACTACGGCCTGATC
AGCTGGCAG





Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
	KS = 65.2203
	KA = 0.2383
	KA/KS = 0.0037
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.