Hello everyone, I need for a project to calculate
dS along branches for
300 house keeping genes within a phylogeny of
The idea is to get a dN/dS distribution of dS for them.
But here is my question, do you think it is better to :
- Build a phylogeny for each house keeping gene and use the corresponding gene tree for the codeml analysis (then the corresponding gene tree is used for each analysis) ?
- Or use a consensus well supported tree of the 100 species for all the analysis (then the same tree is used for all analysis)
The issue I see with the first one is that if I use this one, I will have to constrain the topology of the trees in order to reflect the good topology of speciations using the consensus well supported tree.
Thanks for your help and have a nice day.