diff --git a/src/branch_sequences.c b/src/branch_sequences.c
index a4c775ee..0554e107 100644
--- a/src/branch_sequences.c
+++ b/src/branch_sequences.c
@@ -216,6 +216,7 @@ void carry_unambiguous_gaps_up_tree(newick_node *root)
 		
 		// compare the parent sequence to the each child sequence and update the gaps
 		fill_in_unambiguous_gaps_in_parent_from_children(parent_sequence_index, child_sequence_indices,child_counter);
+		fill_in_unambiguous_bases_in_parent_from_children_where_parent_has_a_gap(parent_sequence_index, child_sequence_indices,child_counter);
 	}
 }
 
diff --git a/src/parse_phylip.c b/src/parse_phylip.c
index 8f4423a8..533da8c4 100644
--- a/src/parse_phylip.c
+++ b/src/parse_phylip.c
@@ -90,6 +90,41 @@ void fill_in_unambiguous_gaps_in_parent_from_children(int parent_sequence_index,
 	}
 }
 
+void fill_in_unambiguous_bases_in_parent_from_children_where_parent_has_a_gap(int parent_sequence_index, int * child_sequence_indices, int num_children)
+{
+	int snp_counter = 0; 
+
+	for(snp_counter = 0; snp_counter < num_snps ; snp_counter++)
+	{
+		if(toupper(sequences[parent_sequence_index][snp_counter]) != 'N' && sequences[parent_sequence_index][snp_counter] != '-')
+		{
+			break;
+		}
+		
+		int real_base_found = 0;
+		int child_counter = 0;
+		char comparison_base ;
+		for(child_counter = 0 ; child_counter < num_children ; child_counter++)
+		{
+			int child_index = child_sequence_indices[child_counter];
+		  if(child_counter == 0)
+			{
+				comparison_base = toupper(sequences[child_index][snp_counter]);
+			}
+		
+			if(comparison_base !=  toupper(sequences[child_index][snp_counter])  )
+			{
+				break;
+			}
+		}
+		
+		if(toupper(sequences[parent_sequence_index][snp_counter]) != comparison_base)
+		{
+			sequences[parent_sequence_index][snp_counter] = comparison_base;
+		}
+	}
+}
+
 int does_column_contain_snps(int snp_column, char reference_base)
 {
 	int i;
diff --git a/src/parse_phylip.h b/src/parse_phylip.h
index 57d9a616..02938c60 100644
--- a/src/parse_phylip.h
+++ b/src/parse_phylip.h
@@ -47,6 +47,8 @@ void load_sequences_from_multifasta_file(char filename[]);
 void set_internal_node(int internal_node_value,int sequence_index);
 void initialise_internal_node();
 int get_internal_node(int sequence_index);
+void fill_in_unambiguous_bases_in_parent_from_children_where_parent_has_a_gap(int parent_sequence_index, int * child_sequence_indices, int num_children);
+void fill_in_unambiguous_gaps_in_parent_from_children(int parent_sequence_index, int * child_sequence_indices, int num_children);
 
 #define MAX_READ_BUFFER 65536
 #define MAX_SAMPLE_NAME_SIZE 1024
diff --git a/tests/check_parse_phylip.c b/tests/check_parse_phylip.c
index a58c3a44..86f0d717 100644
--- a/tests/check_parse_phylip.c
+++ b/tests/check_parse_phylip.c
@@ -69,12 +69,26 @@ START_TEST (phylip_read_in_file_with_gaps)
 }
 END_TEST
 
+START_TEST (phylip_fill_in_unambiguous_bases_in_parent_from_children_where_parent_has_a_gap)
+{
+	load_sequences_from_multifasta_file("../tests/data/alignment_with_gap_in_parent.aln");
+	int child_indices[2] = {0,1};
+	fill_in_unambiguous_bases_in_parent_from_children_where_parent_has_a_gap(2, child_indices, 2);
+	char sequence_bases[10];
+  get_sequence_for_sample_name(sequence_bases, "parent");
+  fail_unless( strcmp(sequence_bases, "AC--") == 0);
+}
+END_TEST
+
+
+
 Suite * parse_phylip_suite(void)
 {
   Suite *s = suite_create ("Parsing a phylip file");
   TCase *tc_phylip = tcase_create ("phylip_files");
   tcase_add_test (tc_phylip, phylip_read_in_small_file);
   tcase_add_test (tc_phylip, phylip_read_in_file_with_gaps);
+  tcase_add_test (tc_phylip, phylip_fill_in_unambiguous_bases_in_parent_from_children_where_parent_has_a_gap);
   suite_add_tcase (s, tc_phylip);
   return s;
 }
diff --git a/tests/data/one_recombination.expected.vcf b/tests/data/one_recombination.expected.vcf
index 88f504eb..2b69521d 100644
--- a/tests/data/one_recombination.expected.vcf
+++ b/tests/data/one_recombination.expected.vcf
@@ -1,11 +1,11 @@
 ##fileformat=VCFv4.1
 ##FORMAT=<ID=AB,Number=1,Type=String,Description="Alt Base">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sequence_1	sequence_2	sequence_3	sequence_4	sequence_5	sequence_6	sequence_7	sequence_8	sequence_9	sequence_10	
-1	1	.	A	C,-,N	.	.	.	AB	A	C	-	-	-	-	-	-	-	A	
-1	6	.	A	-,C,N	.	.	.	AB	A	-	C	-	-	-	-	-	-	A	
-1	8	.	A	-,C,N	.	.	.	AB	A	-	C	-	-	-	-	-	-	A	
-1	9	.	A	-,C,N	.	.	.	AB	A	-	-	C	-	-	-	-	-	A	
-1	11	.	A	-,C,N	.	.	.	AB	A	-	-	C	-	-	-	-	-	A	
+1	1	.	A	C,-	.	.	.	AB	A	C	-	-	-	-	-	-	-	A	
+1	6	.	A	-,C	.	.	.	AB	A	-	C	-	-	-	-	-	-	A	
+1	8	.	A	-,C	.	.	.	AB	A	-	C	-	-	-	-	-	-	A	
+1	9	.	A	-,C	.	.	.	AB	A	-	-	C	-	-	-	-	-	A	
+1	11	.	A	-,C	.	.	.	AB	A	-	-	C	-	-	-	-	-	A	
 1	12	.	A	-,C,N	.	.	.	AB	A	-	-	-	C	-	-	-	-	A	
 1	13	.	A	C,-,N	.	.	.	AB	A	C	-	-	-	-	-	-	-	A	
 1	14	.	A	-,C,N	.	.	.	AB	A	-	-	-	C	-	-	-	-	A