make.simmap very slow

[OKyne1]

Hi Liam and Philip,

Thank you for making this tool!

I am trying to run make.simmap on gene trees which contain many polytomies and zero length branches, but they aren't finishing. They start running but don't complete.

I've been replacing zero length branches with extremely short ones and have tested the tree with and without multi2di( ). In all these tests, make.simmap didn't finish in ~6 hours on a tree with 30 tips and 2 phenotypes.

This is how I was running it: make.simmap(tree, pheno, nsim = 2, model = "ER")

Any advice would be greatly appreciated.

Thank you!
John