Question about population size and generation time

[bingli8899]

Hi,

I am using Simphy for simulating some gene trees. I estimated the substitutions/ coalescent units already and changed our grand truth tree into coalescence unit already. In this case, I am wondering if you have any suggestions about how to set up population size and generation time?

Any suggestions are appreciated!

[bingli8899]

Hi I just want to follow up with my question. For the substitution rate multiplier, I use substitution per site per generation (substitution / (CU * 2Ne)), and I hope to double check if this is what you intended in designing Simphy.

I also hope to check how to specify an outgroup in the species tree. Any help is appreciated!