--- a/src/Makefile.unx
+++ b/src/Makefile.unx
@@ -81,7 +81,6 @@
 #CC        = cc
 #
 #  To use GCC instead:
-CC        = gcc
 #
 # ----------------------------------------------------------------------------
 #
@@ -91,7 +90,6 @@
 #
 #
 #A minimal one
-CFLAGS = 
 #
 # A basic one for debugging
 #CFLAGS  = -g 
@@ -220,7 +218,7 @@
 	@echo "Done."
 	@echo ""
 
-put:
+put: all
 	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
 	@mkdir -p $(EXEDIR)
 	@cp $(PROGS) $(EXEDIR)
@@ -270,195 +268,195 @@
 clique.o:       clique.c disc.h phylip.h
 
 clique:         clique.o disc.o phylip.o
-	$(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
+	$(CC) $(LDFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
 
 cons.o:         cons.c cons.h phylip.h 
 
 consense.o:     consense.c cons.h phylip.h
 
 consense:       consense.o phylip.o cons.o
-	$(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
+	$(CC) $(LDFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
 
 contml.o:       contml.c cont.h phylip.h
 
 contml:       contml.o cont.o phylip.o
-	$(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
+	$(CC) $(LDFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
 
 contrast.o:       contrast.c cont.h phylip.h
 
 contrast:       contrast.o cont.o phylip.o
-	$(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
+	$(CC) $(LDFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
 
 dnacomp.o:      dnacomp.c seq.h phylip.h
 
 dnacomp:      dnacomp.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
+	$(CC) $(LDFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
 
 dnadist.o:      dnadist.c seq.h phylip.h
 
 dnadist:      dnadist.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
+	$(CC) $(LDFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
 
 dnainvar.o:      dnainvar.c seq.h phylip.h
 
 dnainvar:      dnainvar.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
+	$(CC) $(LDFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
 
 dnaml.o:      dnaml.c seq.h phylip.h
 
 dnaml:      dnaml.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
+	$(CC) $(LDFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
 
 dnamlk.o:      dnamlk.c seq.h phylip.h mlclock.h printree.h
 
 dnamlk:      dnamlk.o seq.o phylip.o mlclock.o printree.o
-	$(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
+	$(CC) $(LDFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
 
 dnamove.o:      dnamove.c seq.h moves.h phylip.h
 
 dnamove:      dnamove.o seq.o moves.o phylip.o
-	$(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
+	$(CC) $(LDFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
 
 dnapenny.o:      dnapenny.c seq.h phylip.h
 
 dnapenny:      dnapenny.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
+	$(CC) $(LDFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
 
 dnapars.o:      dnapars.c seq.h phylip.h
 
 dnapars:      dnapars.o seq.o phylip.o
-	$(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
+	$(CC) $(LDFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
 
 dolmove.o:       dolmove.c disc.h moves.h dollo.h phylip.h
 
 dolmove:       dolmove.o disc.o moves.o dollo.o phylip.o
-	$(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
+	$(CC) $(LDFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
 
 dollop.o:       dollop.c disc.h dollo.h phylip.h
 
 dollop:       dollop.o disc.o dollo.o phylip.o
-	$(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
+	$(CC) $(LDFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
 
 dolpenny.o:       dolpenny.c disc.h dollo.h phylip.h
 
 dolpenny:       dolpenny.o disc.o dollo.o phylip.o
-	$(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
+	$(CC) $(LDFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
 
 draw.o:   draw.c draw.h phylip.h 
-	$(CC) $(DFLAGS) -c draw.c
+	$(CC) $(DFLAGS) $(CPPFLAGS) -c draw.c
 
 draw2.o:   draw2.c draw.h phylip.h 
-	$(CC) $(DFLAGS) -c draw2.c
+	$(CC) $(DFLAGS) $(CPPFLAGS) -c draw2.c
 
 drawgram.o:     drawgram.c draw.h phylip.h
-	$(CC) $(DFLAGS) -c drawgram.c
+	$(CC) $(DFLAGS) $(CPPFLAGS) -c drawgram.c
 
 drawgram:     drawgram.o draw.o draw2.o phylip.o
-	$(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
+	$(CC) $(LDFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
 	
 # needed by java	
-libdrawgram.so:   drawgram.o draw.o draw2.o phylip.o
-	$(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
+libdrawgram.so:
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawgram.so -Wl,-soname,libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
 
 drawtree.o:     drawtree.c draw.h phylip.h
-	$(CC) $(DFLAGS)  -shared -fPIC -c drawtree.c
+	$(CC) $(DFLAGS) $(CPPFLAGS) -c drawtree.c
 
 drawtree:     drawtree.o draw.o draw2.o phylip.o
-	$(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
+	$(CC) $(LDFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
 
 # needed by java	
-libdrawtree.so:     drawtree.o draw.o draw2.o phylip.o
-	$(CC) $(CFLAGS) -o libdrawtree.so  -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
+libdrawtree.so:
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawtree.so -Wl,-soname,libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
 
 factor.o:       factor.c phylip.h
 
 factor:       factor.o phylip.o
-	$(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor
+	$(CC) $(LDFLAGS) factor.o phylip.o $(LIBS) -o factor
 
 fitch.o:        fitch.c dist.h phylip.h
 
 fitch:        fitch.o dist.o phylip.o
-	$(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
+	$(CC) $(LDFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
 
 gendist.o:      gendist.c phylip.h
 
 gendist:      gendist.o phylip.o
-	$(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist
+	$(CC) $(LDFLAGS) gendist.o phylip.o $(LIBS) -o gendist
 
 kitsch.o:        kitsch.c dist.h phylip.h
 
 kitsch:        kitsch.o dist.o phylip.o
-	$(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
+	$(CC) $(LDFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
 
 mix.o:        mix.c disc.h wagner.h phylip.h
 
 mix:        mix.o disc.o wagner.o phylip.o
-	$(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
+	$(CC) $(LDFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
 
 move.o:        move.c disc.h moves.h wagner.h phylip.h
 
 move:        move.o disc.o moves.o wagner.o phylip.o
-	$(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
+	$(CC) $(LDFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
 
 neighbor.o:        neighbor.c dist.h phylip.h
 
 neighbor:        neighbor.o dist.o phylip.o
-	$(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
+	$(CC) $(LDFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
 
 pars.o:   pars.c discrete.h phylip.h
 
 pars: pars.o discrete.o phylip.o
-	$(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
+	$(CC) $(LDFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
 
 penny.o:  penny.c disc.h wagner.h phylip.h
 
 penny:  penny.o disc.o wagner.o phylip.o
-	$(CC) $(CFLAGS) penny.o disc.o wagner.o  phylip.o $(LIBS) -o penny
+	$(CC) $(LDFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny
 
 proml.o:      proml.c seq.h phylip.h
 
 proml:      proml.o seq.o phylip.o
-	$(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
+	$(CC) $(LDFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
 
 promlk.o:      promlk.c seq.h phylip.h mlclock.h printree.h
 
 promlk:      promlk.o seq.o phylip.o mlclock.o printree.o
-	$(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
+	$(CC) $(LDFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
 
 protdist.o:      protdist.c seq.h phylip.h
 
 protdist:      protdist.o seq.o phylip.o
-	$(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
+	$(CC) $(LDFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
 
 protpars.o: protpars.c seq.h phylip.h
 
 protpars: protpars.o seq.o phylip.o
-	$(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
+	$(CC) $(LDFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
 
 restdist.o: restdist.c seq.h phylip.h
 
 restdist: restdist.o seq.o phylip.o
-	$(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
+	$(CC) $(LDFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
 
 restml.o: restml.c seq.h phylip.h
 
 restml: restml.o seq.o phylip.o
-	$(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
+	$(CC) $(LDFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
 
 retree.o:       retree.c moves.h phylip.h
 
 retree:       retree.o moves.o phylip.o
-	$(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
+	$(CC) $(LDFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
 
 seqboot.o:      seqboot.c phylip.h
 
 seqboot:      seqboot.o seq.o phylip.o
-	$(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
+	$(CC) $(LDFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
 
 treedist.o:     treedist.c cons.h phylip.h
 
 treedist:     treedist.o phylip.o cons.o
-	$(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
+	$(CC) $(LDFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
 
 
 # ----------------------------------------------------------------------------