fix: pass-through kwargs to TreeTime in arg set up
@@ -61,7 +61,7 @@ def parse_arg(tree1, tree2, aln1, aln2, MCC_file, fill_overhangs=True):
def setup_arg(T, aln, total_mask, segment_mask, dates, MCCs, gtr='JC69',
- verbose=0, fill_overhangs=True, reroot=True, fixed_clock_rate=None):
+ verbose=0, fill_overhangs=True, reroot=True, fixed_clock_rate=None, **kwargs):
"""construct a TreeTime object with the appropriate masks on each node
for branch length optimization with full or segment only alignment.
@@ -83,9 +83,9 @@ def setup_arg(T, aln, total_mask, segment_mask, dates, MCCs, gtr='JC69',
from treetime import TreeTime
tt = TreeTime(dates=dates, tree=T,
- aln=aln, gtr=gtr, verbose=verbose,
+ aln=aln, gtr=gtr, alphabet='nuc', verbose=verbose,
fill_overhangs=fill_overhangs, keep_node_order=True,
- compress=False)
+ compress=False, **kwargs)
if reroot:
