Hi, there,

I am a new guy for molecular evolutionary study. I am now studying a gene which have became pseudogene in some lineages but still functional in other lineages. Here, I want to estimate the evolutionary rate variation between species or lineages contain pseudogene and species or lineages contain functional gene. I expected that the evolutionary rates for species or lineages with pseudogene should greater than species or lineages with functional gene, since relaxed constraint. Thus, what method should I take to carry on such analyses in HyPhy packages?

Best,

Bin :)