A couple improvements to generalize when AA translation is absent.

augur/src/process.py

@@ -72,7 +72,7 @@ def export_to_auspice(self, tree_fields = [], tree_pop_list = []):
 		print "Writing sequences"
 		elems = {}
 		for node in self.tree:
-			if hasattr(node,"clade"):
+			if hasattr(node, "clade") and hasattr(node, "aa_seq"):
 				elems[node.clade] = node.aa_seq
 		write_json(elems, self.auspice_sequences_fname, indent=None)
 

augur/src/tree_refine.py

@@ -59,9 +59,13 @@ def remove_outgroup(self):
 	def collapse(self):
 		"""Collapse edges without mutations to polytomies"""
 		for edge in self.tree.postorder_edge_iter():
-			if edge.tail_node is not None:
-				if edge.is_internal() and edge.head_node.seq==edge.tail_node.seq:
-					edge.collapse()
+			if edge.tail_node is not None and edge.is_internal():
+				if hasattr(edge.head_node, 'seq') and hasattr(edge.tail_node, 'seq'):
+					if edge.head_node.seq==edge.tail_node.seq:
+						edge.collapse()
+				else:
+					if edge.length < 0.00001:
+						edge.collapse()
 
 	def reduce(self):
 		"""

augur/src/virus_clean.py

@@ -50,7 +50,6 @@ def unique_date(self):
 			v.num_date = numerical_date(v.date) + 1e-7*(ii+1)
 
 	def times_from_outgroup(self):
-		self.unique_date()
 		outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
 		return np.array([x.num_date-outgroup_date for x in self.viruses  if x.strain])
 
@@ -82,6 +81,7 @@ def clean_distances(self):
 
 	def clean_generic(self):
 		print "Number of viruses before cleaning:",len(self.viruses)
+		self.unique_date()
 		self.remove_insertions()
 		self.clean_ambiguous()
 		self.clean_distances()