diff --git a/src/Misc/makefile-alpha b/src/Misc/makefile-alpha
index 7b8cbdb..aeaee45 100644
--- a/src/Misc/makefile-alpha
+++ b/src/Misc/makefile-alpha
@@ -16,7 +16,7 @@ INCLUDES = -I$(SRC)
 # Alpha Version
 #
 CC = cc
-CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES)
+CFLAGS = -g  $(INCLUDES)
 ARFLAGS = rv
 
 #
diff --git a/src/abi/makefile-alpha b/src/abi/makefile-alpha
index f200d15..2310ebc 100644
--- a/src/abi/makefile-alpha
+++ b/src/abi/makefile-alpha
@@ -16,9 +16,9 @@ SRC = .
 # Alpha
 #
 CC = cc
-CFLAGS = -g -std1 -ieee_with_inexact -I$(SRC)/../ted
+CFLAGS = -g -I$(SRC)/../ted
 LD = cc
-LDFLAGS = -g -non_shared
+LDFLAGS = -g
 
 #
 # Make the programs
diff --git a/src/alf/makefile-alpha b/src/alf/makefile-alpha
index 7df578e..d7012d8 100644
--- a/src/alf/makefile-alpha
+++ b/src/alf/makefile-alpha
@@ -16,9 +16,9 @@ SRC = .
 # Alpha
 #
 CC = cc
-CFLAGS = -g -std1 -ieee_with_inexact -I$(SRC)/../ted
+CFLAGS = -g  -I$(SRC)/../ted
 LD = cc
-LDFLAGS = -g -non_shared
+LDFLAGS = -g 
 
 
 #
diff --git a/src/bap/makefile-alpha b/src/bap/makefile-alpha
index 7cf135b..c8a3b25 100644
--- a/src/bap/makefile-alpha
+++ b/src/bap/makefile-alpha
@@ -26,13 +26,13 @@ PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
 #
 SRC = .
 STADENSRC=$(SRC)/../staden
-STADENBIN=$(STADENSRC)/alpha-binaries
+STADENBIN=$(STADENSRC)
 TEDSRC=$(SRC)/../ted
-TEDBIN=$(STADENBIN)
+TEDBIN=$(TEDSRC)
 OSPSRC=$(SRC)/osp-bits
-OSPBIN=$(OSPSRC)/alpha-binaries
+OSPBIN=$(OSPSRC)
 MISCSRC=$(SRC)/../Misc
-MISCBIN=$(MISCSRC)/alpha-binaries
+MISCBIN=$(MISCSRC)
 # Use the ted sources compiled for staden executables
 INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
 
@@ -41,18 +41,19 @@ INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
 # Compilers and flags
 #
 CC= cc
-CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES)
-F77= f77
+CFLAGS= -g $(INCLUDES)
+F77= gfortran
 FFLAGS= -g -C
 
-FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil -ldnet_stub
+#FLIBS= -lfor -lUfor  -lots -lFutil
+FLIBS = -lm -lutil  
 XLIBS= -lXaw -lXt -lXmu -lXext -lX11
 LFLAGS= $(FLIBS)
 XLFLAGS= $(XLIBS) $(FLIBS)
 
-LD = f77
+LD = gfortran
 XLD = cc
-LDFLAGS = -g -non_shared
+LDFLAGS = -g
 
 #
 # Avoid compilation of objects in remote directories
@@ -540,28 +541,30 @@ splitp3: $(SPLITP3OBJS)
 # avoid filling up the (small on this machine) /tmp directory
 # with compiler debugging information.
 #
+#%.a: $(SRC)/%.f
+#	BINDIR=`pwd`; \
+#	cd $(SRC); \
+#	SRCDIR=`pwd`; \
+#	TMPDIR=/tmp/staden$$$$; \
+#	if test ! -d $$TMPDIR; \
+#	then mkdir $$TMPDIR; \
+#	fi; \
+#	cd $$TMPDIR; \
+#	rm -f *.f *.o; \
+#	fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
+#	$(F77) $(FFLAGS) -c *.f; \
+#	rm *.f; \
+#	rm -f $$BINDIR/$@; \
+#	ar rcv $$BINDIR/$@ *.o; \
+#	ranlib $$BINDIR/$@; \
+#	rm *.o; \
+#	cd $$BINDIR; \
+#	rm -r $$TMPDIR
+
+
 %.a: $(SRC)/%.f
-	BINDIR=`pwd`; \
-	cd $(SRC); \
-	SRCDIR=`pwd`; \
-	TMPDIR=/tmp/staden$$$$; \
-	if test ! -d $$TMPDIR; \
-	then mkdir $$TMPDIR; \
-	fi; \
-	cd $$TMPDIR; \
-	rm -f *.f *.o; \
-	fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
-	$(F77) $(FFLAGS) -c *.f; \
-	rm *.f; \
-	rm -f $$BINDIR/$@; \
-	ar rcv $$BINDIR/$@ *.o; \
-	ranlib $$BINDIR/$@; \
-	rm *.o; \
-	cd $$BINDIR; \
-	rm -r $$TMPDIR
-
-
-
+	$(F77) $(FFLAGS) -c *.f; 
+	ar rcv $$BINDIR/$@ *.o; 
 
 
 
diff --git a/src/bap/osp-bits/makefile-alpha b/src/bap/osp-bits/makefile-alpha
index a3ccd57..a336b29 100644
--- a/src/bap/osp-bits/makefile-alpha
+++ b/src/bap/osp-bits/makefile-alpha
@@ -23,7 +23,7 @@ VERSION = SUBVERSION
 # Compiler - debug on
 #
 CC= cc
-CFLAGS= -g -non_shared -std1 -ieee_with_inexact -D$(VERSION)
+CFLAGS= -g -D$(VERSION)
 
 
 #
diff --git a/src/convert/makefile-alpha b/src/convert/makefile-alpha
index 30cf237..0a49ee8 100644
--- a/src/convert/makefile-alpha
+++ b/src/convert/makefile-alpha
@@ -4,12 +4,12 @@
 
 SRC = .
 MISCSRC=$(SRC)/../Misc
-MISCBIN=$(MISCSRC)/alpha-binaries
+MISCBIN=$(MISCSRC)
 
 CC = cc
-CFLAGS = -g -std1 -ieee_with_inexact -I$(MISCSRC)
+CFLAGS = -g -I$(MISCSRC)
 LD = cc
-LDFLAGS = -g -non_shared
+LDFLAGS = -g
 LIBS = $(MISCBIN)/misc.a
 
 #
diff --git a/src/cop/makefile-alpha b/src/cop/makefile-alpha
index 26c2255..cc038fc 100644
--- a/src/cop/makefile-alpha
+++ b/src/cop/makefile-alpha
@@ -13,7 +13,7 @@ PROGS = cop cop-bap
 SRC = .
 TEDSRC = $(SRC)/../ted
 MISCSRC = $(SRC)/../Misc
-MISCBIN = $(MISCSRC)/alpha-binaries
+MISCBIN = $(MISCSRC)
 CONVERTSRC = $(SRC)/../convert
 INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC)
 
@@ -21,9 +21,9 @@ INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC)
 # Alpha
 #
 CC = cc
-CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES)
+CFLAGS = -g $(INCLUDES)
 LD = cc
-LDFLAGS = -g -non_shared
+LDFLAGS = -g 
 LIBFLAGS = 
 
 #
diff --git a/src/expGetSeq/makefile-alpha b/src/expGetSeq/makefile-alpha
index af3252c..e1fb49b 100644
--- a/src/expGetSeq/makefile-alpha
+++ b/src/expGetSeq/makefile-alpha
@@ -42,9 +42,9 @@ INCLUDES = -I/usr/include/mit -I$(SRC) -I$(TEDSRC)
 # Compiler - debug on
 #
 CC= cc
-CFLAGS= -g -ieee_with_inexact $(SWITCHES) $(INCLUDES)
+CFLAGS= -g  $(SWITCHES) $(INCLUDES)
 LD= cc
-LDFLAGS= -g -non_shared
+LDFLAGS= -g
 
 
 #
diff --git a/src/frog/makefile-alpha b/src/frog/makefile-alpha
index 3d8bef9..4133818 100644
--- a/src/frog/makefile-alpha
+++ b/src/frog/makefile-alpha
@@ -1,7 +1,7 @@
 CC = cc
-CFLAGS = -g -std1 -ieee_with_inexact
+CFLAGS = -g 
 LD = cc
-LDFLAGS = -g -non_shared
+LDFLAGS = -g
 LIBFLAGS =
 
 SRC = .
diff --git a/src/getMCH/makefile-alpha b/src/getMCH/makefile-alpha
index c8dcb14..085ab8c 100644
--- a/src/getMCH/makefile-alpha
+++ b/src/getMCH/makefile-alpha
@@ -35,9 +35,9 @@ INCLUDES = -I$(SRC) -I$(TEDSRC)
 # Compiler - debug on
 #
 CC= cc
-CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
+CFLAGS= -g $(SWITCHES) $(INCLUDES)
 LD= cc
-LDFLAGS= -g -non_shared
+LDFLAGS= -g
 LIBFLAGS =
 
 
diff --git a/src/indexseqlibs/makefile-alpha b/src/indexseqlibs/makefile-alpha
index f150f63..86d0689 100644
--- a/src/indexseqlibs/makefile-alpha
+++ b/src/indexseqlibs/makefile-alpha
@@ -44,9 +44,9 @@ SRC = .
 # Alpha
 #
 CC = cc
-CFLAGS = -g -std1 -ieee_with_inexact
+CFLAGS = -g
 LD = cc
-LDFLAGS = -g -non_shared
+LDFLAGS = -g
 
 #
 # Shared objects
diff --git a/src/newted/Graph.c b/src/newted/Graph.c
index 0e69bc7..2bf4cac 100644
--- a/src/newted/Graph.c
+++ b/src/newted/Graph.c
@@ -1,4 +1,3 @@
-#include <X11/copyright.h>
 
 /* $XConsortium: Graph.c,v 1.2 88/10/25 17:40:25 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */
diff --git a/src/newted/Graph.h b/src/newted/Graph.h
index 99fe869..c4285c5 100644
--- a/src/newted/Graph.h
+++ b/src/newted/Graph.h
@@ -1,4 +1,3 @@
-#include <X11/copyright.h>
 
 /* $XConsortium: Graph.h,v 1.2 88/10/25 17:22:09 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */
diff --git a/src/newted/GraphP.h b/src/newted/GraphP.h
index 07c673f..62ff7f2 100644
--- a/src/newted/GraphP.h
+++ b/src/newted/GraphP.h
@@ -1,4 +1,3 @@
-#include <X11/copyright.h>
 
 /* $XConsortium: GraphP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */
diff --git a/src/newted/makefile-alpha b/src/newted/makefile-alpha
index e6707b2..faab788 100644
--- a/src/newted/makefile-alpha
+++ b/src/newted/makefile-alpha
@@ -42,11 +42,11 @@ SRC = .
 #
 CC= cc
 INCLUDES = -I$(SRC)
-CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
-LIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub
+CFLAGS= -g  $(SWITCHES) $(INCLUDES)
+LIBS= -lXaw -lXt -lXmu -lXext -lX11 
 #
 LD= cc
-LDFLAGS= -g -non_shared
+LDFLAGS= -g 
 
 #
 # Object files
diff --git a/src/scf/makefile-alpha b/src/scf/makefile-alpha
index 331c209..627ce01 100644
--- a/src/scf/makefile-alpha
+++ b/src/scf/makefile-alpha
@@ -22,9 +22,9 @@ TEDSRC = $(SRC)/../ted
 # alpha
 #
 CC= cc
-CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) -I$(TEDSRC)
+CFLAGS= -g  $(SWITCHES) -I$(TEDSRC)
 LD= cc
-LDFLAGS= -g -non_shared
+LDFLAGS= -g
 LIBFLAGS =
 
 %.o : $(SRC)/%.c
diff --git a/src/staden/makefile-alpha b/src/staden/makefile-alpha
index f9b9043..89af7fd 100644
--- a/src/staden/makefile-alpha
+++ b/src/staden/makefile-alpha
@@ -19,25 +19,25 @@ PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
 SRC=.
 TEDSRC=$(SRC)/../ted
 MISCSRC=$(SRC)/../Misc
-MISCBIN=$(MISCSRC)/alpha-binaries
+MISCBIN=$(MISCSRC)
 INCLUDES= -I$(SRC) -I$(TEDSRC) -I$(MISCSRC)
 
 #
 # Compilers and flags
 #
 CC= cc
-CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES)
-F77= f77
-FFLAGS= -g -C
+CFLAGS= -g $(INCLUDES)
+F77= gfortran
+FFLAGS= -g -fdec -C
 
 FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
 XLIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub
 LFLAGS= $(FLIBS)
 XLFLAGS= $(FLIBS) $(XLIBS) 
 
-LD = f77
+LD = gfortran
 CLD = cc
-LDFLAGS = -g -non_shared # Comment out for faster linking when debugging
+LDFLAGS = -g # Comment out for faster linking when debugging
 
 
 
@@ -549,25 +549,29 @@ vep: $(VEPOBJS)
 # avoid filling up the (small on this machine) /tmp directory
 # with compiler debugging information.
 #
+#%.a:	$(SRC)/%.f
+#	BINDIR=`pwd`; \
+#	cd $(SRC); \
+#	SRCDIR=`pwd`; \
+#	TMPDIR=/tmp/staden$$$$; \
+#	if test ! -d $$TMPDIR; \
+#	then mkdir $$TMPDIR; \
+#	fi; \
+#	cd $$TMPDIR; \
+#	rm -f *.f *.o; \
+#	fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
+#	$(F77) $(FFLAGS) -c *.f; \
+#	rm *.f; \
+#	rm -f $$BINDIR/$@; \
+#	ar rcv $$BINDIR/$@ *.o; \
+#	ranlib $$BINDIR/$@; \
+#	rm *.o; \
+#	cd $$BINDIR; \
+#	rm -r $$TMPDIR
+
 %.a:	$(SRC)/%.f
-	BINDIR=`pwd`; \
-	cd $(SRC); \
-	SRCDIR=`pwd`; \
-	TMPDIR=/tmp/staden$$$$; \
-	if test ! -d $$TMPDIR; \
-	then mkdir $$TMPDIR; \
-	fi; \
-	cd $$TMPDIR; \
-	rm -f *.f *.o; \
-	fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
 	$(F77) $(FFLAGS) -c *.f; \
-	rm *.f; \
-	rm -f $$BINDIR/$@; \
-	ar rcv $$BINDIR/$@ *.o; \
-	ranlib $$BINDIR/$@; \
-	rm *.o; \
-	cd $$BINDIR; \
-	rm -r $$TMPDIR
+	ar rcv *.o
 
 #.f.a:
 #	$(F77) $(FFLAGS) -c $<
diff --git a/src/ted/Graph.c b/src/ted/Graph.c
index 0e69bc7..2bf4cac 100644
--- a/src/ted/Graph.c
+++ b/src/ted/Graph.c
@@ -1,4 +1,3 @@
-#include <X11/copyright.h>
 
 /* $XConsortium: Graph.c,v 1.2 88/10/25 17:40:25 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */
diff --git a/src/ted/Graph.h b/src/ted/Graph.h
index 99fe869..0b36bd0 100644
--- a/src/ted/Graph.h
+++ b/src/ted/Graph.h
@@ -1,5 +1,3 @@
-#include <X11/copyright.h>
-
 /* $XConsortium: Graph.h,v 1.2 88/10/25 17:22:09 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */
 
@@ -44,38 +42,35 @@
 
 /* define any special resource names here that are not in <X11/StringDefs.h> */
 
-#define XtNgraphResource		"graphResource"
-#define XtCGraphResource		"GraphResource"
-
-#define XtNdimBackground                "dimBackground"
-#define XtNexposeCallback               "exposeCallback"
-#define XtNgraphColour1                 "graphColour1"
-#define XtNgraphColour2                 "graphColour2"
-#define XtNgraphColour3                 "graphColour3"
-#define XtNgraphColour4                 "graphColour4"
-#define XtNresizeCallback               "resizeCallback"
+#define XtNgraphResource "graphResource"
+#define XtCGraphResource "GraphResource"
 
+#define XtNdimBackground "dimBackground"
+#define XtNexposeCallback "exposeCallback"
+#define XtNgraphColour1 "graphColour1"
+#define XtNgraphColour2 "graphColour2"
+#define XtNgraphColour3 "graphColour3"
+#define XtNgraphColour4 "graphColour4"
+#define XtNresizeCallback "resizeCallback"
 
 /* declare specific GraphWidget class and instance datatypes */
 
-typedef struct _GraphClassRec  *GraphWidgetClass;
-typedef struct _GraphRec       *GraphWidget;
-
+typedef struct _GraphClassRec *GraphWidgetClass;
+typedef struct _GraphRec *GraphWidget;
 
 /* declare the class constant */
 
 extern WidgetClass graphWidgetClass;
 
-
 /* ---- Exported procedures ---- */
 
 extern Pixel GraphColour1(Widget w);
 extern Pixel GraphColour2(Widget w);
 extern Pixel GraphColour3(Widget w);
 extern Pixel GraphColour4(Widget w);
-extern GC    GraphGC1(Widget w);
-extern GC    GraphGC2(Widget w);
-extern GC    GraphGC3(Widget w);
-extern GC    GraphGC4(Widget w);
+extern GC GraphGC1(Widget w);
+extern GC GraphGC2(Widget w);
+extern GC GraphGC3(Widget w);
+extern GC GraphGC4(Widget w);
 
 #endif /* _Graph_h */
diff --git a/src/ted/GraphP.h b/src/ted/GraphP.h
index 07c673f..62ff7f2 100644
--- a/src/ted/GraphP.h
+++ b/src/ted/GraphP.h
@@ -1,4 +1,3 @@
-#include <X11/copyright.h>
 
 /* $XConsortium: GraphP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */
diff --git a/src/ted/makefile-alpha b/src/ted/makefile-alpha
index e571a12..dbcc3c2 100644
--- a/src/ted/makefile-alpha
+++ b/src/ted/makefile-alpha
@@ -33,13 +33,14 @@ SRC = .
 #
 # Compiler - debug on
 #
-CC= cc
+CC= gfortran
 INCLUDES = -I$(SRC)
-CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
-LIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub
+CFLAGS= -g $(SWITCHES) $(INCLUDES)
+LIBS= -lXaw -lXt -lXmu -lXext -lX11 
+#-ldnet_stub
 #
-LD= cc
-LDFLAGS= -g -non_shared
+LD= gfortran
+LDFLAGS= -g 
 
 #
 # Object files
diff --git a/src/update_subclones/makefile-alpha b/src/update_subclones/makefile-alpha
index 7f1782d..a24c246 100644
--- a/src/update_subclones/makefile-alpha
+++ b/src/update_subclones/makefile-alpha
@@ -12,16 +12,16 @@ PROGS = update_subclones
 #
 SRC = .
 MISCSRC = $(SRC)/../Misc
-MISCBIN = $(MISCSRC)/alpha-binaries
+MISCBIN = $(MISCSRC)
 INCLUDES = -I$(SRC) -I$(MISCSRC)
 
 #
 # Alpha
 #
 CC = cc
-CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES)
+CFLAGS = -g $(INCLUDES)
 LD = cc
-LDFLAGS = -g -non_shared
+LDFLAGS = -g 
 
 #
 # Here they are
diff --git a/src/vepe/makefile-alpha b/src/vepe/makefile-alpha
index ff9fb35..f06a9f8 100644
--- a/src/vepe/makefile-alpha
+++ b/src/vepe/makefile-alpha
@@ -21,7 +21,7 @@ all: $(PROGS)
 SRC = .
 #STADENSRC=/nfs/rutland/home3/pubseq/inhouse/share/src/staden
 STADENSRC=$(SRC)/../staden
-STADENBIN=$(STADENSRC)/alpha-binaries
+STADENBIN=$(STADENSRC)
 # Use the ted sources compiled for staden executables
 INCLUDES= -I$(STADENSRC)
 
@@ -31,11 +31,11 @@ INCLUDES= -I$(STADENSRC)
 #
 # debug on
 CC= cc
-CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES)
-F77= f77
+CFLAGS= -g $(INCLUDES)
+F77= gfortran
 FFLAGS= -g
-LD= f77
-LDFLAGS= -g -non_shared
+LD= gfortran
+LDFLAGS= -g 
 
 FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
 XLIBS= -lXaw -lXt -lXmu -lXext -lX11