fixes in get_reconstructed_alignment
@@ -1509,7 +1509,7 @@ class TreeAnc(object):
self.infer_ancestral_sequences()
if self.data.is_sparse:
- new_aln = {'sequences': {n.name: self.data.compressed_to_sparse_sequence(node.cseq)
+ new_aln = {'sequences': {n.name: self.data.compressed_to_sparse_sequence(n.cseq)
for n in self.tree.find_clades()}}
new_aln['reference'] = self.data.ref
new_aln['positions'] = self.data.nonref_positions
@@ -1522,7 +1522,7 @@ class TreeAnc(object):
def get_tree_dict(self, keep_var_ambigs=False):
- return self.reconstructed_alignment()
+ return self.get_reconstructed_alignment()
def recover_var_ambigs(self):
"""
