Tools for genome-wide population genetics analysis

Question

[GR]

Hi everyone,

I am looking for a tool to get genome-wide DN/DS and PN/PS ratios. I used DnaSp but it works only for a small set of genes. I have created the alignments for all the genes of my species of interest. Does anyone knows a tool/package that can be used to get these ratios on all the genes in a genome.

Thanks,
RT

Answer 1

[Brice Sarver]

codeml in PAML, but you'll need to generate many input files and loop across them. A lot of CPUs or a cluster will be your friend here. I use it for exome-scale datasets.

HyPhy can be a bit of a pain to use due to poor documentation, but you may be able to speed up your analyses using FUBAR.

Hope this helps. I'd appreciate other suggestions, too, if you stumble upon any that are at least as sophisticated as codeml.

Edit: this popped up in my open list, and I didn't see that it was quite a few weeks old. Didn't mean to necro but hope it helps nevertheless.

[GR]

Hi Brice,

Thanks a lot for your help. I calculated DN/DS and PN/PS ratios using egglib library. Very fast and made it easy to do for whole genome. Hope this will help someone else as well. http://www.biomedcentral.com/1471-2156/13/27