We corresponded with Carolina offline, but here I'm including a generalized
solution of the quick solution we just sent her in case it's useful for
others (avoiding the issue lampooned in https://xkcd.com/979/).
The data was a delimited file with a species column and columns for each
character,
Hi Liam and everyone
The numbers from this message "1000 trees with a mapped discrete character
with states: 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,
44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55" are the same numbers from
the nodes on my tree. As I replied to Brian, I assumed
Hi Carolina.
I agree with Brian that a Q matrix in which the elements of a row are
all zeros is not likely to be you problem. It just means that the ML
estimated transition rate from 1->0, in your case, is zero.
I agree with Brian that the message "1000 trees with a mapped discrete
