diff -ur probaligngui_beta_1.3.orig//probalign/src/Main.cc probaligngui_beta_1.3//probalign/src/Main.cc
--- probaligngui_beta_1.3.orig//probalign/src/Main.cc	2010-08-17 14:10:21.238544093 -0500
+++ probaligngui_beta_1.3//probalign/src/Main.cc	2010-08-17 16:15:54.968544093 -0500
@@ -14,6 +14,8 @@
 #include <iomanip>
 #include <iostream>
 #include <cerrno>
+#include <climits>
+#include <cstring>
 
 //struct for column reliability
 
Only in probaligngui_beta_1.3//probalign/src: Main.cc.orig
Only in probaligngui_beta_1.3//probalign/src: Main.cc.porig
Only in probaligngui_beta_1.3//probalign/src: Main.cc.rej
diff -ur probaligngui_beta_1.3.orig//probalign/src/PostProbs.cc probaligngui_beta_1.3//probalign/src/PostProbs.cc
--- probaligngui_beta_1.3.orig//probalign/src/PostProbs.cc	2010-08-17 14:10:21.238544093 -0500
+++ probaligngui_beta_1.3//probalign/src/PostProbs.cc	2010-08-17 16:22:24.618544093 -0500
@@ -6,6 +6,7 @@
 #include <time.h>
 #include <ctype.h>
 #include <assert.h>
+#include <cstdio>
 #define  TRACE 0		// 0: NOTRACE 1: TRACE
 
 //proba like settings