Recommendations for dN/dS software for balancing selection scan

Question

[dthorbur]

I am looking to systematically scan genomes for balancing selection. However, I am going to be doing this analysis within a species, with 66 replicates. In doing so, I have been recommended to stay away from programs that typically are used for analyses across species.

Does anyone have a suggestion for dN/dS software to use for between population analysis?

Thanks for your time.

[Martombo]

I'm no expert but I'm wondering how should the computation be different for inter and intra-species analyses and why a typical tool like PAML wouldn't be suitable. You can check this discussion to see if it helps: Best Practices/Softwares To Calculate Ka/Ks Ratio

[dthorbur]

I think this issue has been resolved. It appears to have been a misunderstanding between a bioinformatician and myself. I believe they were concerned about the ML tree, rather than actually calculating the ratio. Since I have such a big data set, we are going to use RAxML or ExaML to generate the ML tree and either HyPhy or potentially the ETE Toolkit to calculate the dN/dS ratio. Though, a lot of background reading is necessary before choosing.

[Martombo]

thanks for following up

Answer 1

[h.mon]

Although PAML is probably the gold standard for this kind of analysis, it is kind of awkward to script around it and its output is considered painful to parse (I never personally did so). The ETE Toolkit is really nice and flexible for programmatically performing such tasks, with the added benefit of offering good documentation and pretty graphical output.

[dthorbur]

Thanks for point this out. I've just looked into using HyPhy since it seems to be able to handle hyper-polymorphic regions well - such as the MHC gene region. But I'll look into the ETE Toolkit as at a glance, it looks like it might be much easier to implement.