diff --git a/configure.ac b/configure.ac
index cc5e631..5abbd23 100644
--- a/configure.ac
+++ b/configure.ac
@@ -10,7 +10,7 @@ PKG_CHECK_MODULES([CHECK],[check >= 0.8.2],[have_check="yes"],
   AC_MSG_WARN(["'Check' unit testing framework not found. It would be impossible to run unit tests!"])
   [have_check="no"])
 
-AC_CHECK_HEADERS([zlib.h math.h])
+AC_CHECK_HEADERS([zlib.h math.h getopt.h])
 AC_CHECK_LIB(m, floor)
 AX_CHECK_ZLIB
 
diff --git a/src/Makefile.am b/src/Makefile.am
index 9d5773b..a4ddd4f 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -3,6 +3,7 @@ snpsitesinclude_HEADERS=alignment-file.h  vcf.h phylib-of-snp-sites.h snp-sites.
 
 bin_PROGRAMS = snp-sites
 snp_sites_SOURCES = main.c
+snp_sites_CFLAGS = --std=c99
 snp_sites_LDADD = libsnp-sites.la -lpthread
 
 # libsnp_sites.so is our library
diff --git a/src/main.c b/src/main.c
index 1c67070..53358e3 100644
--- a/src/main.c
+++ b/src/main.c
@@ -23,6 +23,7 @@
 #include <string.h>
 #include <ctype.h>
 #include <unistd.h>
+#include <getopt.h>
 #include "snp-sites.h"
 #include "config.h"
 
@@ -91,7 +92,7 @@ int main (int argc, char **argv) {
   {
     print_usage();
   }
-    
+
 	return 0;
 }