allowing 'fixed_pi' to be passed to infer_gtr from TreeTime.run()
@@ -102,6 +102,8 @@ class TreeTime(ClockTree):
"""
# determine how to reconstruct and sample sequences
seq_kwargs = {"marginal":False, "sample_from_profile":"root"}
+ if "fixed_pi" in kwargs:
+ seq_kwargs["fixed_pi"] = kwargs['fixed_pi']
if "do_marginal" in kwargs:
time_marginal=kwargs["do_marginal"]
