Implications for species tree height

[zhao shen]

Hi ! 

First, thank you for accepting my request for joining the group! Thanks a lot for the SimPhy program that is very user friendly. 

Here is my question : 

I want to use -ST * parameter in simphy to simulate different ILS levels, but I don't know what ST means for species tree height. How do I know my species tree height. And how to set the size of the simulated species tree height.

• -ST *: Species tree height (time units).

Could anyone help me understand that? Thank you!

[Diego M.]

I am glad you are finding SimPhy easy to use.

The ST parameter indicates the height of the tree in time units (e.g., 100 M years) used to simulate the species tree. This parameter, in combination with the other parameters of the species tree simulation process (e.g., birth or birth and death rate), will generate a certain distribution of branch lengths.

The amount of ILS in the simulated scenario will depend on the locus tree branch lengths measured in coalescent units. This is a function of the number of generations (time/generation time) and the population size (coalescent unit = 2 * population size * generations; for diploid organisms, half for haploid)

I hope this helps,

DM