--- file_not_specified_in_diff	
+++ file_not_specified_in_diff	
@@ -, +, @@ 
--- a/align/Amap.cc
+++ b/align/Amap.cc
@@ -12,6 +12,8 @@ 
 #include "ProbabilisticModel.h"
 #include "EvolutionaryTree.h"
 #include "SparseMatrix.h"
+#include <limits>
+#include <climits>
 #include <string>
 #include <sstream>
 #include <iomanip>
@@ -23,6 +25,7 @@ 
 #include <cstdlib>
 #include <cerrno>
 #include <iomanip>
+#include <cstring>
 
 string parametersInputFilename = "";
 string parametersOutputFilename = "no training";
--- a/align/MultiSequenceDag.h
+++ b/align/MultiSequenceDag.h
@@ -13,6 +13,7 @@ 
 #include <map>
 #include <queue>
 #include <iostream>
+#include <limits>
 #include "MultiSequence.h"
 #include "SparseMatrix.h"