PAL2NAL output

CLUSTAL W multiple sequence alignment

PHR_ECOLI.    ATGACTACCCATCTGGTCTGGTTTCGCCAGGATTTACGTCTGCACGATAATCTCGCACTG
PHR_SALTY.    ATGCCCACCCATTTAGTCTGGTTCAGGCGCGATCTGCGTTTACAGGATAACCTTGCGCTG

PHR_ECOLI.    GCTGCCGCCTGCCGCAATTCGTCTGCACGCGTGCTGGCGTTGTATATCGCTACACCACGC
PHR_SALTY.    GCCGCCGCCTGCCGCGATGCATCCGCGCGGGTGCTGGCGCTTTATATTTCCACCCCCGCG

PHR_ECOLI.    CAGTGGGCGACGCATAACATGTCGCCGCGTCAGGCTGAACTTATCAATGCTCAACTGAAT
PHR_SALTY.    CAGTGGCAGGCCCATGATATGGCGCCGCGGCAGGCGGCATTCATCAGCGCGCAGCTCAAT

PHR_ECOLI.    GGGCTACAAATAGCGCTTGCGGAAAAAGGTATTCCTTTATTGTTCCGTGAAGTGGATGAC
PHR_SALTY.    GCGCTACAGACGGCCCTTGCAGAGAAAGGCATTCCGTTGCTGTTTCATGAAGTGGCGGAT

PHR_ECOLI.    TTTGTCGCCAGTGTCGAAATAGTTAAACAGGTGTGCGCGGAAAACAGCGTTACCCACCTG
PHR_SALTY.    TTTAACGCCAGTATTGAAACGGTCAAAAACGTTTGCCGACAGCATGACGTCAGCCATCTG

PHR_ECOLI.    TTTTATAACTATCAGTATGAAGTGAATGAGCGGGCGCGGGATGTGGAAGTTGAAAGAGCG
PHR_SALTY.    TTTTATAACTATCAGTATGAGTTTAACGAGCGTCAGCGTGATGCGGCGGTGGAAAAAACG

PHR_ECOLI.    CTGCGTAACGTGGTGTGTGAAGGATTTGATGACAGCGTGATCCTGCCGCCTGGCGCGGTG
PHR_SALTY.    CTGCCCTCTGTCATCTGCGAAGGCTTTGACGATAGCGTGATTCTGGCGCCCGGCGCGGTG

PHR_ECOLI.    ATGACCGGTAATCACGAGATGTACAAAGTCTTTACGCCTTTTAAGAATGCCTGGCTGAAA
PHR_SALTY.    ATGACCGGCAATCATGAAATGTATAAAGTTTTTACGCCGTTTAAAAATGCCTGGTTGAAA

PHR_ECOLI.    CGGCTGCGGGAAGGGATGCCGGAGTGCGTCGCTGCGCCAAAAGTTCGTAGTAGCGGATCG
PHR_SALTY.    CGGCTAAAAGAAGATATCCCGCCGTGCGTTCCGGCCCCGAAGATCCGGGTGAGCGGCGCG

PHR_ECOLI.    ATAGAGCCCTCGCCATCCATTACGCTGAATTATCCTCGTCAGTCTTTCGATACTGCGCAT
PHR_SALTY.    CTTTCTCCCTTAACGCCAGTCTCGCTTAACTACCCGCAACAGGCGTTTGACGCCGCGCTT

PHR_ECOLI.    TTTCCGGTGGAAGAAAAAGCGGCGATTGCGCAATTACGCCAGTTTTGCCAGAACGGTGCC
PHR_SALTY.    TTCCCGGTGGAAGAAAACGCGGTCATCGCGCAGCTACGTCAGTTTTGCGCGCAGGGCGCA

PHR_ECOLI.    GGAGAATATGAGCAACAACGAGATTTTCCGGCAGTGGAAGGCACCAGCCGTTTGTCGGCC
PHR_SALTY.    GACGAGTATGCGTTACGGCGCGATTTCCCTGCGGTTGACGGCACCAGTCGGCTTTCCGCC

PHR_ECOLI.    AGCCTGGCAACGGGCGGGTTATCGCCTCGCCAGTGCTTGCATCGCTTGTTGGCTGAACAG
PHR_SALTY.    AGCCTGGCGACGGGCGGCCTGTCGCCGCGACAGTGCCTGCACCGATTACTGGCGGAGCAG

PHR_ECOLI.    CCGCAGGCGCTGGACGGTGGGGCCGGTAGTGTCTGGCTTAATGAGCTGATCTGGCGCGAG
PHR_SALTY.    CCGCAGGCGCTGGACGGCGGGCCGGGAAGCGTCTGGTTGAATGAGCTCATCTGGCGGGAA

PHR_ECOLI.    TTTTACCGTCACCTGATAACGTATCACCCCTCGTTGTGTAAACATCGTCCATTTATTGCC
PHR_SALTY.    TTTTACCGTCATTTAATGACCTGGTATCCGGCATTATGCAAACACCAGCCGTTTATCCGC

PHR_ECOLI.    TGGACGGATCGTGTACAGTGGCAGAGCAATCCCGCACATTTACAGGCCTGGCAGGAAGGC
PHR_SALTY.    TGGACAAAACGCGTCGCGTGGCAGGAAAACCCGCACTATTTTCAGGCATGGCAGAAAGGC

PHR_ECOLI.    AAAACGGGATACCCGATTGTTGATGCCGCTATGCGTCAGCTTAACAGCACTGGCTGGATG
PHR_SALTY.    GAAACCGGTTATCCCATTGTCGATGCGGCGATGCGCCAGCTTAACGCGACGGGCTGGATG

PHR_ECOLI.    CATAACAGGCTACGGATGATTACAGCCAGTTTTCTGGTGAAAGATTTATTGATCGACTGG
PHR_SALTY.    CATAACCGTTTACGCATGATTACCGCCAGCTTTCTGGTAAAAGATCTGTTGATTGACTGG

PHR_ECOLI.    CGCGAAGGCGAGCGATATTTCATGTCGCAGCTGATTGATGGTGATTTGGCAGCCAATAAC
PHR_SALTY.    CGGTTGGGGGAGCGCTATTTCATGTCGCAGCTTATTGACGGCGATCTTGCCGCCAATAAT

PHR_ECOLI.    GGTGGCTGGCAGTGGGCCGCTTCAACCGGAACCGATGCAGCGCCGTATTTTCGTATTTTC
PHR_SALTY.    GGCGGCTGGCAGTGGGCCGCCTCAACCGGTACTGACGCCGCGCCTTATTTTCGTATTTTT

PHR_ECOLI.    AACCCGACAACCCAGGGCGAGAAATTTGATCATGAGGGCGAGTTTATCCGCCAGTGGCTA
PHR_SALTY.    AATCCCACGACTCAGGGAGAGAGGTTCGATCGCGACGGCGAATTTATCCGCCAGTGGCTA

PHR_ECOLI.    CCGGAACTGCGCGATGTGCCAGGGAAAGTGGTGCATGAGCCGTGGAAGTGGGCGCAGAAA
PHR_SALTY.    CCGGCATTACGCGATATCCCTGGAAAAGCGATTCACGAGCCGTGGCGGTGGGCGGAAAAA

PHR_ECOLI.    GCAGGTGTGACGCTGGATTATCCGCAACCGATAGTCGAGCACAAAGAAGCGAGAGTACAA
PHR_SALTY.    GCGGGAGTCGTGCTTGATTATCCTCGGCCTATTGTGGAGCACAAACAGGCGAGAATCGCA

PHR_ECOLI.    ACGTTGGCAGCGTATGAGGCGGCGCGGAAGGGGAAA
PHR_SALTY.    ACGCTTTCCGCCTATGAGGCGGCGAGAAAAGGGGCG



Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
KS = 1.9232
KA = 0.1322
KA/KS = 0.0687
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.