What Type Of Analyses Are Used To Characterize The Co-Evolution Of Genes?

Question

[Pappu]

I am analyzing the co-evolution of a set of functionally related genes starting from bacteria to eukaryotes. Other than making phylogenetic trees and MSAs, is there any review or list of basic analysis that can be done?

I am sorry for not being so specific. I simply want to know the state of art in this area rather than starting with a hypothesis.

[Josh Herr]

Could you please be a little more specific with what you are trying to do? The methodology is quite different whether you are talking about co-evolution between a host & parasite or co-evolution between a protein and receptor or co-evolution of interacting genes within a single lineage.

[aidan-budd]

Yes, reiterating Josh's comment - giving more specific details of the kinds of questions you'd be interested in asking would make it easier to suggest possible tools/approaches. While trying to formulate these questions, it might help to ask yourself "What would be an exciting result I might expect to see from my analysis?"

Answer 1

[Whetting]

check out this paper
Syst Biol. 2002 Apr;51(2):217-34.
A statistical test for host-parasite coevolution.
Legendre P, Desdevises Y, Bazin E.

Axparafit is the more computationally friendly version of the software