--- Makefile.orig	Thu Jan 25 13:59:21 2007
+++ Makefile	Thu Jan 25 14:02:58 2007
@@ -1,11 +1,6 @@
 LIBS    = -lm
 BINDIR  = ./bin
-#CFLAGS  = -Wall -Wshadow -g
-CFLAGS  = -O -Wall -Wshadow -g
-#CFLAGS  = -fast -inline speed
-#CFLAGS  = -O3 -arch host -fast
-CC        = gcc $(CFLAGS)
-#CC        = cc $(CFLAGS)
+CFLAGS += -g
 DCC     = gcc -g -Wall -DDMALLOC_FUNC_CHECK -ansi -pedantic
 PLUSCC    = g++ $(CFLAGS)
 LIBS   = -lm -L/usr/local/lib
@@ -18,29 +13,29 @@
 # The big banana
 recombine : recombine.o jdrop.o rec_modellike.o jworld.o getdata.o \
 	traitlike.o getmsatdata.o
-	$(CC) -o recombine recombine.o jdrop.o rec_modellike.o \
+	$(CC) $(CFLAGS) -o recombine recombine.o jdrop.o rec_modellike.o \
 	jworld.o getdata.o traitlike.o getmsatdata.o $(LIBS)
 
 jworld.o : jworld.c
-	$(CC) -c jworld.c
+	$(CC) $(CFLAGS) -c jworld.c
 
 jdrop.o : jdrop.c
-	$(CC) -c jdrop.c
+	$(CC) $(CFLAGS) -c jdrop.c
 
 rec_modellike.o : rec_modellike.c
-	$(CC) -c rec_modellike.c
+	$(CC) $(CFLAGS) -c rec_modellike.c
 
 recombine.o : recombine.c
-	$(CC) -c recombine.c 
+	$(CC) $(CFLAGS) -c recombine.c 
 
 getdata.o : getdata.c
-	$(CC) -c getdata.c
+	$(CC) $(CFLAGS) -c getdata.c
 
 getmsatdata.o : getmsatdata.c
-	$(CC) -c getmsatdata.c
+	$(CC) $(CFLAGS) -c getmsatdata.c
 
 traitlike.o : traitlike.c
-	$(CC) -c traitlike.c
+	$(CC) $(CFLAGS) -c traitlike.c
 
 rectreedna : rectreedna.c
 	$(CC) -o rectreedna rectreedna.c $(LIBS)