--- a/Makefile.in
+++ b/Makefile.in
@@ -1,7 +1,11 @@
-PREFIX			= /usr/local/bin
+prefix			= @prefix@
+exec_prefix		= @exec_prefix@
+bindir			= @bindir@
 TEST				= test/
-CC					= gcc  
-CFLAGS			= -O9  -Wall 
+CC				= @CC@  
+CFLAGS			= @CFLAGS@
+CPPFLAGS		= @CPPFLAGS@
+LDFLAGS			= @LDFLAGS@
 DEBUGFLAGS		= -ggdb -Wall 
 
 SOURCES			= kalign2_distance_calculation.c kalign2_dp.c kalign2_input.c kalign2_main.c kalign2_mem.c kalign2_inferface.c kalign2_misc.c kalign2_tree.c  kalign2_profile.c kalign2_alignment_types.c kalign2_feature.c kalign2_hirschberg.c  kalign2_advanced_gaps.c kalign2_hirschberg_dna.c  kalign2_output.c kalign2_string_matching.c kalign2_profile_alignment.c 
@@ -16,10 +20,7 @@
 .PHONY: clean
 
 all: $(OBJECTS)
-	$(CC) $(CFLAGS) $(OBJECTS) -o $(PROGS)
-	
-%.o:	%.c
-	$(CC) $(CFLAGS) -c $<
+	$(CC) $(LDFLAGS) $(CFLAGS) $(OBJECTS) -o $(PROGS)
 	
 debug: $(DEBUGOBJECTS)
 	$(CC) $(DEBUGFLAGS) $(DEBUGOBJECTS) -o $(DEBUGPROGS)	
@@ -29,7 +30,8 @@
 
 
 install:
-	cp $(PROGS) /usr/local/bin/
+	mkdir -p $(DESTDIR)$(bindir)
+	cp $(PROGS) $(DESTDIR)$(bindir)
 	
 clean: 
 	rm -f $(PROGS) $(OBJECTS)