Is there any tool to calculate dn/ds for orthologues?
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7.2 years ago
ThulasiS ▴ 90

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

sequence R alignment KaKs • 4.2k views
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7.2 years ago
Rahul Sharma ▴ 660

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.

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7.2 years ago
Lila M ★ 1.3k

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 ;)

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