add 'marginal' keyword argument along 'marginal_sequences' in TreeTime.run
@@ -136,6 +136,7 @@ class TreeTime(ClockTree):
"branch_length_mode": self.branch_length_mode,
"sample_from_profile":"root",
"reconstruct_tip_states":kwargs.get("reconstruct_tip_states", False)}
+ seq_kwargs["marginal"] = seq_kwargs["marginal_sequences"]
tt_kwargs = {'clock_rate':fixed_clock_rate, 'time_marginal':False}
tt_kwargs.update(kwargs)
