Makefile                            |    8 +++---
 scripts/Makefile                    |    6 +++-
 scripts/aln2wig/Makefile            |    8 +++---
 scripts/compileSpliceCands/Makefile |    6 ++--
 src/Makefile                        |   43 ++++++++++++++++++----------------
 5 files changed, 38 insertions(+), 33 deletions(-)

diff --git a/Makefile b/Makefile
index e23a667..64610c8 100644
--- a/Makefile
+++ b/Makefile
@@ -3,9 +3,9 @@
 #
 
 all: 
-	cd src && ${MAKE}
-	cd scripts && ${MAKE}
+	$(MAKE) -C src
+	$(MAKE) -C scripts
 
 clean: 
-	cd src && ${MAKE} clean
-	cd scripts && ${MAKE} clean
+	$(MAKE) -C src clean
+	$(MAKE) -C scripts clean
diff --git a/scripts/Makefile b/scripts/Makefile
index 6d4dd67..ab6a885 100644
--- a/scripts/Makefile
+++ b/scripts/Makefile
@@ -1,5 +1,7 @@
 all :
-	cd aln2wig && ${MAKE}
+	$(MAKE) -C aln2wig
+	$(MAKE) -C compileSpliceCands
 
 clean : 
-	cd aln2wig && ${MAKE} clean
+	$(MAKE) -C aln2wig clean
+	$(MAKE) -C compileSpliceCands
diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile
index 64d09f5..9752980 100644
--- a/scripts/aln2wig/Makefile
+++ b/scripts/aln2wig/Makefile
@@ -1,10 +1,10 @@
-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb
+CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic
 
 psl2wig : aln2wig.o
-	gcc $(CFLAGS) -o aln2wig aln2wig.o;
-	cp aln2wig ../../bin
+	$(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o;
+	cp aln2wig ../../bin/
 psl2wig.o : aln2wig.c
-	gcc $(CFLAGS) -c aln2wig.c
+	$(CC) $(CFLAGS) -c aln2wig.c
 
 all : psl2wig
 
diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile
index cddada5..8079791 100644
--- a/scripts/compileSpliceCands/Makefile
+++ b/scripts/compileSpliceCands/Makefile
@@ -1,8 +1,8 @@
 compileSpliceCands : compileSpliceCands.o list.h list.o
-	gcc -o compileSpliceCands compileSpliceCands.o list.o;
-#	cp compileSpliceCands ../../bin
+	$(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o;
+	cp compileSpliceCands ../../bin/
 compileSpliceCands.o : compileSpliceCands.c 
-	gcc -Wall -pedantic -ansi -c compileSpliceCands.c 
+	$(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c 
 
 all : compileSpliceCands
 
diff --git a/src/Makefile b/src/Makefile
index 71795b6..732b953 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -6,8 +6,8 @@
 #          a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
 #        - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
 #        
-CC	= g++
-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG  -g -ggdb -static
+CXX	?= g++
+CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG  -g -ggdb -static
 INCLS	= -I../include -I.
 LIBS	= # -lcwd
 OBJS	= genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \
@@ -18,45 +18,48 @@ TOBJS	= commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte
 PROGR	= augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign
 INFO    = cflags
 
-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info
+all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin
 
 .SUFFIXES:
 .SUFFIXES: .cc .o .so
 
 .cc.o:
-	$(CC) -c $(CFLAGS) -o $@ $< $(INCLS) 
+	$(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS) 
 
-augustus: augustus.cc $(OBJS) $(DUMOBJS)
-	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+bin: $(PROGR)
+	cp $(PROGR) ../bin/
+
+augustus: augustus.o $(OBJS) $(DUMOBJS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp augustus ../bin/
 
-etraining: etraining.cc $(TOBJS) $(OBJS) 
-	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+etraining: etraining.o $(TOBJS) $(OBJS) 
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp etraining ../bin/
 
-evaluate: evaluate.cc $(OBJS) $(DUMOBJS)
-	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+evaluate: evaluate.o $(OBJS) $(DUMOBJS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 
-consensusFinder: consensusFinder.cc consensus.o 
-	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+consensusFinder: consensusFinder.o consensus.o 
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 
-curve2hints: curve2hints.cc exon_seg.o 
-	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+curve2hints: curve2hints.o exon_seg.o 
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 
-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \
+fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \
 	types.o properties.o geneticcode.o pp_profile.o lldouble.o
-	$(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp fastBlockSearch ../bin/
 
-prepareAlign: pp_prepare_align.cc
-	$(CC) $(CFLAGS) -o $@ $^
+prepareAlign: pp_prepare_align.o
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^
 	cp prepareAlign ../bin/
 
 info:
-	echo "$(CFLAGS)" > $(INFO)
+	echo "$(CXXFLAGS)" > $(INFO)
 
 clean:
-	rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o  $(INFO) 
+	rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o  $(INFO) ../bin/*
 
 tidy: clean
 	rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO)