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diff --git a/Makefile b/Makefile
index 0802f65..3816b6e 100644
--- a/Makefile
+++ b/Makefile
@@ -2,9 +2,9 @@ VERSION=1.0.0
MINOR_VER=20140314
CC=gcc
ifdef DEBUG
-CFLAGS=-g3 -W -Wall -O0 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3
+CFLAGS=-g3 -W -Wall -O0 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
else
-CFLAGS=-W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3
+CFLAGS=-W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
endif
INSTALLDIR=/usr/local/bin
GLIBS=-lm -lpthread
diff --git a/ksw.c b/ksw.c
index 15dd0f2..22641ed 100644
--- a/ksw.c
+++ b/ksw.c
@@ -25,7 +25,7 @@
#include <stdlib.h>
#include <stdint.h>
-#include <emmintrin.h>
+#include "sse2neon.h"
#include "ksw.h"
#ifdef USE_MALLOC_WRAPPERS
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