avoid conversion to upper case in mugration
@@ -96,9 +96,11 @@ if __name__=="__main__":
###########################################################################
### set up treeanc
###########################################################################
- treeanc = TreeAnc(params.tree, gtr=mugration_GTR, verbose=params.verbose, one_mutation=0.001)
+ treeanc = TreeAnc(params.tree, gtr=mugration_GTR, verbose=params.verbose,
+ convert_upper=False, one_mutation=0.001)
pseudo_seqs = [SeqRecord(id=n.name,name=n.name,
- seq=Seq(reverse_alphabet[leaf_to_attr[n.name]] if n.name in leaf_to_attr else missing_char))
+ seq=Seq(reverse_alphabet[leaf_to_attr[n.name]]
+ if n.name in leaf_to_attr else missing_char))
for n in treeanc.tree.get_terminals()]
treeanc.aln = MultipleSeqAlignment(pseudo_seqs)
