diff --git a/src/Newickform.c b/src/Newickform.c
index 0214f788..e35c2ee6 100644
--- a/src/Newickform.c
+++ b/src/Newickform.c
@@ -191,26 +191,26 @@ newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp
 	root = parseTree(pcTreeStr);
 	
 	// output tab file
-    FILE * block_file_pointer;
-    char block_file_name[MAX_FILENAME_SIZE] = {""};
-    char block_file_extension[5]= {".tab"};
+  FILE * block_file_pointer;
+  char block_file_name[MAX_FILENAME_SIZE] = {""};
+  char block_file_extension[5]= {".tab"};
 	memcpy(block_file_name, filename, size_of_string(filename) +1);
 	concat_strings_created_with_malloc(block_file_name,block_file_extension);
 	block_file_pointer = fopen(block_file_name, "w");
 	
 	// output tab file
-    FILE * branch_snps_file_pointer;
-    char branch_snps_file_name[MAX_FILENAME_SIZE]= {""};
-    char branchtab_extension[18]= {".branch_snps.tab"};
+  FILE * branch_snps_file_pointer;
+  char branch_snps_file_name[MAX_FILENAME_SIZE]= {""};
+  char branchtab_extension[18]= {".branch_snps.tab"};
 	memcpy(branch_snps_file_name, filename, size_of_string(filename) +1);
 	concat_strings_created_with_malloc(branch_snps_file_name,branchtab_extension);
 	branch_snps_file_pointer = fopen(branch_snps_file_name, "w");
 	
 	// output gff file
 	FILE * gff_file_pointer;
-    char gff_file_name[MAX_FILENAME_SIZE]= {""};
-    memcpy(gff_file_name, filename, size_of_string(filename) +1);
-    char gff_extension[5]= {".gff"};
+  char gff_file_name[MAX_FILENAME_SIZE]= {""};
+  memcpy(gff_file_name, filename, size_of_string(filename) +1);
+  char gff_extension[5]= {".gff"};
 	concat_strings_created_with_malloc(gff_file_name,gff_extension);
 	gff_file_pointer = fopen(gff_file_name, "w");
 	print_gff_header(gff_file_pointer,length_of_original_genome);
@@ -307,25 +307,6 @@ newick_node* build_newick_tree(char * filename, FILE *vcf_file_pointer,int * snp
 
   }
   
-//  char * root_sequence = NULL;
-//	root_sequence = generate_branch_sequences(root,
-//                                              vcf_file_pointer,
-//                                              snp_locations,
-//                                              number_of_snps,
-//                                              column_names,
-//                                              number_of_columns,
-//                                              root_sequence,
-//                                              length_of_original_genome,
-//                                              block_file_pointer,
-//                                              gff_file_pointer,
-//                                              min_snps,
-//                                              branch_snps_file_pointer,
-//                                              window_min,
-//                                              window_max,
-//                                              uncorrected_p_value,
-//                                              trimming_ratio,
-//                                              extensive_search_flag);
-//	free(root_sequence);
   free(nodeArray);
   free(node_depths);
   free(node_sequences);