Hyphy Vs Codeml

Question

[GR]

Hello Everyone,

I am new to phylogenetics and currently doing selection analysis for few genes of interest from different species. My question is whether I should use HyPhy or codeml for my dataset and if both tools are build for same purpose and can deal with both intra and inter-species dataset then which one is more reliable in my case.

Thanks, RT

Answer 1

[Joseph Hughes]

Both HYPHY and codeml are designed to measure selection in sequences, however codeml offers some models and parameters not available in HYPHY and vice versa. For example, MEME (mixed effects models of evolution) have recently been incorporated into HyPhy see this reference. To me, it seems that the two programs are used by different communities. When I was working on whole organisms stuff, colleagues around me used codeml and now that I am working on viruses, most researcher seem to use HyPhy. HyPhy has the additional advantage of the DataMonkey server, removing the pain of installation.

[QVINTVS_FABIVS_MAXIMVS]

Three of those authors teach my bioinformatics class. lol