can anybody help me out calculating dn/ds for nucleotide sequences? I have around 788 nucleotide sequence and corresponding amino acid sequences. I have also calculated codon usage table ysing CUSP (EMBOSS package). I have installed paml, codeml, SNAP and hyphy. In case of SNAP, I could not identify how to give our own genetic code table? In hyphy I could not decide which module to use either MEME or other? and the major problem is how to generate input files for HYPHY? Can anybody help me out doing such analysis?