Simulating contained coalescent trees on ML tree with Bas in substitutions/site

[walz.d...@gmail.com]

Hello,

I'm working on some simulations of reads from genomic data that includes a coalescent component.

I have been using treesim.contained_coalescent_tree to simulate gene genealogies constrained by a ML species tree from RAxML (and it works great). However, I'm concerned about the BLs being in substitutions, not coalescent units, and was wondering if setting the edge population sizes to one would make sense in this instance? I believe I can do this as follows:

for edge in sp_tree.postorder_edge_iter(): 
      edge.pop_size = 1.0

I saw this suggestion on a previous question, but the alternative BLs mentioned were generations, not substitutions, so I wanted to check and see if this still made sense or if you had any other suggestions. 

Thank you very much for your time and for the very useful package.

Best,

Chad