Hi everyone,

HyPhy is new for me and I often get confused over even little things. Maybe my question is very basic, but I was not able to find an answer myself.

Is it possible to use HyPhy to analyze gene families dynamics?

Pretty much I have the species tree and number of gene families from genomes of corresponding species. I also have determined phylogeny for every gene family. Now I want to find out what rates of gene duplication, gene loss and HGT for every branch of species tree for every gene family fit my data the best. Is that possible to do using HyPhy?

Thank you all very much.

Hi there,

HyPhy is probably not the easiest solution for your analysis as it does not have pre-written tools to do topology comparisons and infer duplication/loss etc events. It all CAN be done, but only by writing some batch code.

Sergei