PAL2NAL output

CLUSTAL W multiple sequence alignment

Hsor          atgaggtctttggtgcttctctgtgttttgctgatggcaatatgtgcggcggacaaaaaa
Hruf          atgaggtctttggtgcttctctgtgttttgctgatggcaatatgtgcggcggacaaaaaa

Hsor          accacggtctcgaaggaaaatgcagccgcaatgaagatagctatgataaagtttttggat
Hruf          tccacggtctcgaaggaaaatgcagccgcaatgaaggtagcgatgataaagtttttggat

Hsor          gcgagggcgggtaaattcaaaaaacgcgttgagaatatgggatatccaataacccctccg
Hruf          tcgaggacggatagattcaaaaaacgcattgagaagattggatatccaataacccctccg

Hsor          caatggacaactctactatactacaacagacagagattgatggaatggtgccatacctac
Hruf          caatatacaactctactatactacaacagagagagattgatggattggtgccataactac

Hsor          gttgaattttccaaaaagattatattgatgggaggtaacaaattaaataagaagaacttc
Hruf          gttgaagtatccaaaaagattatattgttgggaggtaacaaattaaataagaagaacttc

Hsor          actaggatgggtcgaatcattggctggaaaaaccagtgggttttgaaaaggaggcaatgg
Hruf          gctaggatgggtcgaatcattggctggaaaaaccagtggattttgaaaaggaggcaatgg

Hsor          gagatggtcagagtgatgaggcgctataaaagtactgcaatagctaaaaagatcgtcgcc
Hruf          cacatggtcagagtgatgaggcgctataaagcttctgcaatagctaaaaagatcgtcgcc

Hsor          atgaaagttgctgacctaccctgtaac
Hruf          atgaaagttgctgacctaccctgtaac

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 0.0131
	K_A = 0.0718
	K_A/K_S = 5.4660
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.