gravatar for Chvatil

2 hours ago by

Hello everyone, I need for a project to calculate dS along branches for 300 house keeping genes within a phylogeny of 100 species.

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.

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