diff --git a/bwt_gen/Makefile b/bwt_gen/Makefile
deleted file mode 100644
index a7fe6cf4..00000000
--- a/bwt_gen/Makefile
+++ /dev/null
@@ -1,23 +0,0 @@
-CC=			gcc
-CFLAGS=		-g -Wall -O2 -m64 # comment out `-m64' for 32-bit compilation
-DFLAGS=		-D_FILE_OFFSET_BITS=64
-OBJS=		bwt_gen.o QSufSort.o
-INCLUDES=	
-VERSION=	0.1.0
-LIBS=		
-SUBDIRS=
-
-.SUFFIXES:.c .o
-
-.c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
-lib:libbwtgen.a
-
-libbwtgen.a:$(OBJS)
-		$(AR) -scru $@ $(OBJS)
-
-cleanlocal:
-		rm -f gmon.out *.o a.out $(PROG) *~ *.a
-
-clean:cleanlocal