diff --git a/Makefile b/Makefile
index fbbbe79..a1d449b 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
 all:
-	(cd src; $(MAKE))
+	$(MAKE) -C src
 clean:
 	rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
 	(cd src; $(MAKE) clean)
diff --git a/src/Makefile b/src/Makefile
index 7f6b6fd..dd6309b 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W
 TRGT_DIR = ..
 
 all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
-	(cd glocal; $(MAKE))
+	$(MAKE) -C glocal
 clean: 
 	rm -f *.o *~ utils/*~ mlagan.purify core
 	(cd glocal; $(MAKE) clean)
 ../anchors: anchors.c skiplist.c
-	$(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
 ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
-	$(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
 ../order: order.c diagmatrix.c filebuffer.c
-	$(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
 ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
-	$(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
 ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
-	$(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
 ../utils/bin2mf: utils/bin2mf.c
-	$(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
 ../utils/bin2bl: utils/bin2bl.c
-	$(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
 ../utils/cextract: utils/cextract.c
-	$(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
 ../utils/cstat: utils/cstat.c
-	$(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
 ../utils/contigorder: utils/contigorder.c
-	$(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
 ../utils/getbounds: utils/getbounds.c
-	$(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
 ../utils/getcontigpos: utils/getcontigpos.c
-	$(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
 ../utils/getlength: utils/getlength.c
-	$(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
 ../utils/getoverlap: utils/getoverlap.c
-	$(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
 ../utils/rc: utils/rc.c
-	$(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
 ../utils/seqmerge: utils/seqmerge.c
-	$(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
 ../utils/scorealign: utils/scorealign.c
-	$(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
 ../utils/scorecontigs: utils/scorecontigs.c
-	$(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
 ../utils/fa2xfa: utils/fa2xfa.c
-	$(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
 ../utils/overlay: utils/overlay.c
-	$(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
 ../utils/Glue: utils/Glue.cpp
-	$(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
 ../utils/dotplot: utils/dotplot.cpp
-	$(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
diff --git a/src/glocal/Makefile b/src/glocal/Makefile
index ce1421a..b82507f 100755
--- a/src/glocal/Makefile
+++ b/src/glocal/Makefile
@@ -10,10 +10,10 @@ TRGT = glocal
 OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
 
 .cpp.o:
-	$(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
+	$(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp
 
 $(TRGT): $(OBJECTS)
-	$(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
+	$(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
 
 clean :
 	rm -f *.o ./*~ *~ core