diff --git a/RE_sites.py b/RE_sites.py
index 9c1e40c..7a63ce5 100755
--- a/RE_sites.py
+++ b/RE_sites.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python2
 
 import re 
 import sys
diff --git a/alignments2txt.py b/alignments2txt.py
index 382d2b7..be8c755 100755
--- a/alignments2txt.py
+++ b/alignments2txt.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python2
+
 import os,sys
 import argparse
 import pickle
diff --git a/break_contigs.cpp b/break_contigs.cpp
old mode 100755
new mode 100644
diff --git a/break_contigs_start.cpp b/break_contigs_start.cpp
old mode 100755
new mode 100644
diff --git a/cmdline.h b/cmdline.h
old mode 100755
new mode 100644
diff --git a/correct.py b/correct.py
index 9f3e75a..678f922 100755
--- a/correct.py
+++ b/correct.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python2
+
 import sys
 
 #reads input assembly, breakpoints given by the method and outputs new contig file with lengths
diff --git a/correct_links.cpp b/correct_links.cpp
old mode 100755
new mode 100644
diff --git a/fast_scaled_scores.py b/fast_scaled_scores.py
index 3b2a2ad..633f9a8 100755
--- a/fast_scaled_scores.py
+++ b/fast_scaled_scores.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python2
+
 import networkx as nx
 import sys
 import argparse
@@ -86,4 +88,4 @@ def get_max_weight(start,end):
    #print str(u)+'\t'+str(v)+'\t'+str(w)+'\t'+str(bestAlt)+'\t'+str(w/bestAlt)+'\t'+str("FALSE")+'\t'+str("FALSE")+'\t'+str("FALSE")
    #print "%s %s %f %f %f %d %s %s"%(u, v, d, bestAlt, d/bestAlt, G[u][v]['links'],G[u][v]['isNeighbor'], G[u][v]['isGood'])
 ofile.close()
-f1.close()
\ No newline at end of file
+f1.close()
diff --git a/get_seq.py b/get_seq.py
index 399ef07..9161f31 100755
--- a/get_seq.py
+++ b/get_seq.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python2
+
 import pickle
 import argparse
 
diff --git a/layout_unitigs.py b/layout_unitigs.py
index d2964b9..a1d1efa 100755
--- a/layout_unitigs.py
+++ b/layout_unitigs.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python2
+
 import networkx as nx
 import sys
 import operator
diff --git a/make_links.py b/make_links.py
index b953f66..d6fc949 100755
--- a/make_links.py
+++ b/make_links.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python2
+
 import operator
 import math
 import sys
diff --git a/refactor_breaks.py b/refactor_breaks.py
index a16a4a9..695ffa9 100755
--- a/refactor_breaks.py
+++ b/refactor_breaks.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python2
+
 import os,sys
 import argparse
 import pickle
diff --git a/run_pipeline.py b/run_pipeline.py
old mode 100644
new mode 100755
index c73a42d..25d0195
--- a/run_pipeline.py
+++ b/run_pipeline.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python2
+
 import os
 import stat
 import argparse
diff --git a/stitch.py b/stitch.py
index 6ce12f7..a231da0 100755
--- a/stitch.py
+++ b/stitch.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python2
+
 import argparse,pickle
 
 parser = argparse.ArgumentParser()