AlignedFragment.cc | 1 +
 AlignedFragment.h  | 2 ++
 Assert.cc          | 2 +-
 Assert.h           | 4 ++--
 Block.cc           | 1 +
 Main.cc            | 1 +
 MultiSequence.cc   | 2 +-
 PairAligner.cc     | 2 ++
 ProbModel.cc       | 3 ++-
 9 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/AlignedFragment.cc b/AlignedFragment.cc
index b553862..9c734b9 100644
--- a/AlignedFragment.cc
+++ b/AlignedFragment.cc
@@ -2,6 +2,7 @@
 //
 //////////////////////////////////////////////////////////////////////
 
+#include <stdlib.h>
 #include "AlignedFragment.h"
 #include "Assert.h"
 #include "Utilities.h"
diff --git a/AlignedFragment.h b/AlignedFragment.h
index ffc4642..17ae615 100644
--- a/AlignedFragment.h
+++ b/AlignedFragment.h
@@ -8,6 +8,8 @@
 #define ALIGNFRAGMENT_H
 
 #include <vector>
+#include <string.h>
+#include <stdio.h>
 
 class Fragment;
 class AlignedFragment;
diff --git a/Assert.cc b/Assert.cc
index ac9a7df..449e00a 100644
--- a/Assert.cc
+++ b/Assert.cc
@@ -10,7 +10,7 @@
 // Write out assertion error message
 //////////////////////////////////////////////////////////////////////
 
-int _ASSERT_FAILED (char *filename, int line_number, const char *error_msg){
+int _ASSERT_FAILED (const char *filename, int line_number, const char *error_msg){
   fprintf (stderr, "Assertion failed in file \"%s\", line %d: %s\n",
 	   filename, line_number, error_msg);
   abort();
diff --git a/Assert.h b/Assert.h
index 0222d17..069705b 100644
--- a/Assert.h
+++ b/Assert.h
@@ -10,9 +10,9 @@
 int _ASSERT_FAILED (char *filename, int line_number, const char *error_msg);
 
 #ifdef NDEBUG
-#define ASSERT(test,error_msg)
+#define ASSERT(test, error_msg)
 #else
-#define ASSERT(test,error_msg) (test ? 0 : _ASSERT_FAILED(__FILE__, __LINE__, error_msg))
+#define ASSERT(test, error_msg) (test ? 0 : _ASSERT_FAILED(__FILE__, __LINE__, error_msg))
 #endif
   
 #endif
diff --git a/Block.cc b/Block.cc
index 35b050d..a24ad0e 100644
--- a/Block.cc
+++ b/Block.cc
@@ -2,6 +2,7 @@
 //
 //////////////////////////////////////////////////////////////////////
 
+#include <stdlib.h>
 #include "Block.h"
 #include "AlignedFragment.h"
 #include "Sequence.h"
diff --git a/Main.cc b/Main.cc
index 8ceded3..7cf1b75 100644
--- a/Main.cc
+++ b/Main.cc
@@ -5,6 +5,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
+#include <limits.h>
 #include <vector>
 #include "Assert.h"
 #include "MultiSequence.h"
diff --git a/MultiSequence.cc b/MultiSequence.cc
index 86e493f..2b70723 100644
--- a/MultiSequence.cc
+++ b/MultiSequence.cc
@@ -386,7 +386,7 @@ void MultiSequence::WriteMFA (FILE *file) const {
 //////////////////////////////////////////////////////////////////////
 
 const char MultiSequence::ComputeAnnotation (const char *data, const int size) const {
-  static char *groups[47] = {
+  static const char *groups[47] = {
     
     // Identities
     "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", 
diff --git a/PairAligner.cc b/PairAligner.cc
index 7fdc21f..8bbc4a5 100644
--- a/PairAligner.cc
+++ b/PairAligner.cc
@@ -4,6 +4,8 @@
 // Implementation of PairAligner class
 ////////////////////////////////////////////////////////////////////
 
+#include <string.h>
+#include <stdlib.h>
 #include "PairAligner.h"
 #include "Utilities.h"
 #include "LocalAlign.h"
diff --git a/ProbModel.cc b/ProbModel.cc
index 6d74e3d..5d5a838 100644
--- a/ProbModel.cc
+++ b/ProbModel.cc
@@ -4,6 +4,7 @@
 
 #include <stdio.h>
 #include <ctype.h>
+#include <string.h>
 #include "ProbModel.h"
 #include "Utilities.h"
 
@@ -30,7 +31,7 @@ const int TRANSITIONS[NUM_STATES][NUM_STATES] = {
   { 0, 0, 0, 0, 0, 0, 1 }
 };
 
-char *ALPHABET = "ARNDCQEGHILKMFPSTWYV";
+const char *ALPHABET = "ARNDCQEGHILKMFPSTWYV";
 
 
 float INIT_A = 0.9860202074;