Dear @rneher ,
Please see below:
DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving
polytomies using the old 'greedy' mode. This is not well suited for large
polytomies. Stochastic resolution will become the default in future
versions. To switch now, rerun with the flag --stochastic-resolve. To
keep using the greedy method in the future, run with --greedy-resolve
Best,
Liam