specifying number of rate categories for species-specific heterogeneity

[august_guang]

Is it possible to specify a specific number of categories for species-specific heterogeneity, as well as which branches they go on? From the manual it looks like a value from Gamma(alpha, 1/alpha) is drawn for every branch, but what if I want to specify one rate (or distribution) for one set of branches and a different rate for a different set of branches?

[Diego M.]

Dear August,

The current version of SimPhy does not allow to specify sampling strategies with different species-specific heterogeneity distributions/categories for different species tree branches. Nevertheless, there would be an easy shortcut if you knew how to program.

a) Simulate species trees with SimPhy (or another simulator/library)

b) Write a script to sample species-specific rates following the parameterization scheme you want (with a specific number of categories associated to different sets of branches, if I understood well) .

c) Run SimPhy a second time, using the previously simulated species trees as input incorporating the sampled species-specific rates for each branch using the u_mult (Nexus) or * (extended Newick) branch modifier.

I hope this helps,

              Diego M.