diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..f66d2b6
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,31 @@
+CXX=	g++
+
+BIN = $(DESTDIR)/usr/bin
+# With pthreads
+override FLAGS+= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 -march=native
+# Without pthreads
+#override FLAGS+= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 -march=native
+
+THREAD=	-lpthread
+
+SOURCE = align dbseq main pairs param reads utilities
+OBJS1= $(patsubst %,%.o,$(SOURCE))
+
+all: bsmap
+%.o:%.cpp
+	$(CXX) $(FLAGS) -c $< -o $@
+bsmap: $(OBJS1)
+	(cd samtools; make)
+	(cd gzstream; make)
+	$(CXX) $(FLAGS) $^ -o $@ $(THREAD) -lbam -lz -lgzstream
+	rm -f *.o
+
+clean:
+	rm -f *.o *~ bsmap
+	(cd samtools; make clean)
+	(cd gzstream; make clean)
+install:
+	install -d $(BIN)
+	install ./bsmap $(BIN)
+	install ./sam2bam.sh $(BIN)
+	install ./methratio.py $(BIN)
diff --git a/makefile b/makefile
deleted file mode 100644
index 62e0dfc..0000000
--- a/makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-CC=	g++
-
-BIN = $(DESTDIR)/usr/bin
-FLAGS= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64
-#FLAGS= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -g -m64
-#FLAGS= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -Wall -Wno-strict-aliasing -m64
-
-
-THREAD=	-lpthread
-
-SOURCE = align dbseq main pairs param reads utilities
-OBJS1= $(patsubst %,%.o,$(SOURCE))
-
-all: bsmap
-%.o:%.cpp
-	$(CC) $(FLAGS) -c $< -o $@
-bsmap: $(OBJS1)
-	(cd samtools; make)
-	(cd gzstream; make)
-	$(CC) $(FLAGS) $^ -o $@ $(THREAD) -lbam -lz -lgzstream
-	rm -f *.o
-
-clean:
-	rm -f *.o *~ bsmap
-	(cd samtools; make clean)
-	(cd gzstream; make clean)
-install:
-	install -d $(BIN)
-	install ./bsmap $(BIN)
-	install ./sam2bam.sh $(BIN)
-	install ./methratio.py $(BIN)