Calculate Dn/Ds for nucleotide sequences using codeml, hyphy or SNAP.
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9 weeks ago

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?

Paml codeml SNAP hyphy • 215 views
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I have experience with codeml. Do you have any problems with it?

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No, I have no problem with CodeML. Your help will really be appreciated. I had RAST annotated protein sequences and corresponding nucleotide sequences having same headers. I have installed CodeML. Can you please guide me how to go ahead with codeML?

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You cannot calculate dN/dS if you have only sequences of your species. For each gene you should have a sequence of at least one homolog in another species, or, which is better, in two other species. I recommend to have at least three sequences for each gene:
1) One for the gene of your species.
2) One for some closely related species.
3) One for a more phylogenetically distant species that will be used as the outgroup.

Then you need to build a multiple sequence alignment for each gene. After that, you must provide codeml with this multiple alignment and a phylogenetic tree of these three species. You can read a more detailed description of what you will have to do here.

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Yeah, I have orthologs of those genes in around 800 other strains. I have also done MSA using clustalw. But what next. I have made a pahylogeny of each genes like file.ph. what to do for codeml?

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What to do next depends on the goal of you work. For example, if you're interested in dN/dS values in one particular strain, you should run codeml with the branch model. Codeml will produce dN/dS values for all branches, including the terminal branch of the strain you're interested in. All necessary details are provided in the manual of PAML

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Thank you so much for your reply. Let me go through it.

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