diff --git a/Makefile b/Makefile
index 53e5c5b..a2d3feb 100644
--- a/Makefile
+++ b/Makefile
@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
 all: 	$(PROGS) tRNAscan-SE setpaths
 
 covels-SE:  $(OBJ) scan_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
 
 coves-SE: $(OBJ) score_main.o
-	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
 
 eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
-	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
+	$(CC) $(CFLAGS)  $(LDFLAGS) -o eufindtRNA eufind_main.o \
 	pavesi.o $(SQUIDOBJ) $(LIBS)
 
 trnascan-1.4: trnascan.o
-	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
+	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c
 
 tRNAscan-SE:
 	$(PERLDIR)/$(PERLBIN) checkversion.pl