prune short branches even when not optizing branch length
@@ -27,8 +27,8 @@ class TreeTime(ClockTree):
# initially, infer ancestral sequences and infer gtr model if desired
if use_input_branch_length:
- self.infer_ancestral_sequences(infer_gtr=infer_gtr,
- prune_short=True, **seq_kwargs)
+ self.infer_ancestral_sequences(infer_gtr=infer_gtr, **seq_kwargs)
+ self.prune_short_branches()
else:
self.optimize_sequences_and_branch_length(infer_gtr=infer_gtr,
max_iter=2, prune_short=True, **seq_kwargs)
@@ -46,7 +46,7 @@ class TreeTime(ClockTree):
self.reroot(root=root)
if use_input_branch_length:
- self.infer_ancestral_sequences(prune_short=False, **seq_kwargs)
+ self.infer_ancestral_sequences(**seq_kwargs)
else:
self.optimize_sequences_and_branch_length(max_iter=2,**seq_kwargs)
