Is there any tool to calculate dn/ds for orthologues?

Question

[ThulasiS]

Hi all

I am trying to calculate dn/ds ratio for several genes. I am trying to analyze the selection pressure on several bacterial genes. I have 12 bacterial genomes and 1600 gene clusters i.e. gene1 in all 12 species and gene2 in all 12 species and so on.. I would like to calculate dn/ds for all genes. I tried KaKs calculator, R script and other tools but all are for pair of sequences only. Any suggestion will be deeply appreciated.

Thank you

Answer 1

[Rahul Sharma]

Few years ago I used the codeml module of PAML tool to carry out selection analyses on several fungal species Published_work. There are several models (site model, branch-site model, branch model and clade model) that one could select on the basis of your aim of the analysis. You can detect selection pressure including data from multiple species.

Answer 2

[Lila M]

You can estimate the dN/dS ratio at individual codons using different methods implemented in the HYPHY program (SLAC, FEL, IFEL, FUBAR) an also you can use the amilo-Bianchi- Li method as implemented in MEGA to measure the ratio between the mean number of dN and dS nucleotide substitutions per site (dN /dS ). I assume that this packages are also implemented in R, just have a look in to them ;)