--- Makefile.orig	Wed Oct 25 23:39:34 2000
+++ Makefile	Mon Aug  6 16:13:02 2001
@@ -1,105 +1,37 @@
 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
 DLIBS   = -lm -L/usr/local/lib -ldmalloc
 CGCC    = checkergcc -g -Wall
 CGLIBS  = -lm
-# -O
 PROGS   =           recombine
 
 # 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
-
-rectreedna : rectreedna.c
-	$(CC) -o rectreedna rectreedna.c $(LIBS)
-
-hapdna : hapdna.c
-	$(CC) -o hapdna hapdna.c $(LIBS)
-
-mhapdna : mhapdna.c
-	$(CC) -o mhapdna mhapdna.c $(LIBS)
-
-drecombine.o : recombine.c
-	$(CC) -o drecombine.o -c recombine.c
-
-djdrop.o : jdrop.c
-	$(CC)  -o djdrop.o -c jdrop.c
-
-drec_modellike.o : rec_modellike.c
-	$(CC) -o drec_modellike.o -c rec_modellike.c
-
-djworld.o : jworld.c
-	$(CC) -o djworld.o -c jworld.c
-
-dgetdata.o : getdata.c
-	$(CC) -o dgetdata.o -c getdata.c
-
-dgetmsatdata.o : getmsatdata.c
-	$(CC) -o dgetmsatdata.o -c getmsatdata.c
-
-drecombine:  drecombine.o djdrop.o drec_modellike.o djworld.o dgetdata.o memdebug.o memalpha.o memfree.o \
-        dgetmsatdata.o
-	$(CC) drecombine.o djdrop.o drec_modellike.o djworld.o dgetdata.o memdebug.o memalpha.o memfree.o \
-	dgetmsatdata.o $(LIBS) -o drecombine
-
-dclean: 
-	rm drecombine.o djdrop.o drec_modellike.o djworld.o dgetdata.o dgetmsatdata.o
-
-clean :
-	rm -f *.o
-
-gentrees.o : gentrees.c
-	$(CC) -c gentrees.c
-
-segtre_mig.o : segtre_mig.c
-	$(CC) -c segtre_mig.c
-
-rectree : gentrees.o segtre_mig.o
-	$(CC) gentrees.o segtre_mig.o $(LIBS) -o rectree
-
-jrectree : simrectree.c
-	$(CC) simrectree.c $(LIBS) -o jrectree
-
-snp : snp.c
-	$(CC) snp.c $(LIBS) -o snp
-
-panelmaker : panelmaker.c
-	$(CC) panelmaker.c $(LIBS) -o panelmaker
-
-variance : variance.c
-	$(CC) variance.c $(LIBS) -o variance
-
-distree : distree.c
-	$(CC) distree.c $(LIBS) -o distree
+	$(CC) $(CFLAGS) -c traitlike.c