diff --git a/src/Misc/makefile b/src/Misc/makefile
new file mode 100644
index 0000000..aeaee45
--- /dev/null
+++ b/src/Misc/makefile
@@ -0,0 +1,52 @@
+#
+# Makefile for Miscellaneous routines - Alpha version 
+
+#
+# Objects made by this makefile
+#
+LIBS = misc.a
+
+#
+# Where the wild things are
+#
+SRC = .
+INCLUDES = -I$(SRC)
+
+#
+# Alpha Version
+#
+CC = cc
+CFLAGS = -g  $(INCLUDES)
+ARFLAGS = rv
+
+#
+# Objects
+#
+OBJS = \
+	crash.o \
+	date.o \
+	filenames.o \
+	files.o \
+	find.o \
+	shell.o \
+	strings.o
+
+#
+# Main dependency
+#
+$(LIBS) : $(OBJS)
+	/bin/rm -f $(LIBS) ;\
+	$(AR) $(ARFLAGS) $(LIBS) $(OBJS) ;\
+	ranlib $(LIBS)
+
+
+#
+# Special dependencies
+#
+%.o : $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+all : $(LIBS)
+
+clean :
+	/bin/rm -f $(OBJS) $(LIBS)
diff --git a/src/Misc/makefile-alpha b/src/Misc/makefile-alpha
index aeaee45..7b8cbdb 100644
--- a/src/Misc/makefile-alpha
+++ b/src/Misc/makefile-alpha
@@ -16,7 +16,7 @@ INCLUDES = -I$(SRC)
 # Alpha Version
 #
 CC = cc
-CFLAGS = -g  $(INCLUDES)
+CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES)
 ARFLAGS = rv
 
 #
diff --git a/src/abi/makefile b/src/abi/makefile
new file mode 100644
index 0000000..b0275d9
--- /dev/null
+++ b/src/abi/makefile
@@ -0,0 +1,43 @@
+#
+# Makefile for abi - Alpha version
+#
+
+#
+# Programs made by this makefile
+#
+PROGS = getABISampleName 2rs
+all: $(PROGS)
+
+#
+# Where the wild things are
+#
+SRC = .
+
+#
+# Alpha
+#
+CC = cc
+CFLAGS = -g -I$(SRC)/../ted
+LD = cc
+LDFLAGS = -g
+
+#
+# Make the programs
+#
+getABISampleName: getABISampleName.o
+	$(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o
+
+2rs: 2rs.o
+	$(LD) $(LDFLAGS) -o 2rs 2rs.o
+
+#
+# Special dependencies
+#
+
+%.o : $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+all: $(PROGS)
+
+clean:
+	/bin/rm -f $(PROGS) *.o *~
diff --git a/src/abi/makefile-alpha b/src/abi/makefile-alpha
index b0275d9..f200d15 100644
--- a/src/abi/makefile-alpha
+++ b/src/abi/makefile-alpha
@@ -5,8 +5,7 @@
 #
 # Programs made by this makefile
 #
-PROGS = getABISampleName 2rs
-all: $(PROGS)
+PROGS = getABISampleName
 
 #
 # Where the wild things are
@@ -17,9 +16,9 @@ SRC = .
 # Alpha
 #
 CC = cc
-CFLAGS = -g -I$(SRC)/../ted
+CFLAGS = -g -std1 -ieee_with_inexact -I$(SRC)/../ted
 LD = cc
-LDFLAGS = -g
+LDFLAGS = -g -non_shared
 
 #
 # Make the programs
@@ -27,8 +26,6 @@ LDFLAGS = -g
 getABISampleName: getABISampleName.o
 	$(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o
 
-2rs: 2rs.o
-	$(LD) $(LDFLAGS) -o 2rs 2rs.o
 
 #
 # Special dependencies
diff --git a/src/alf/makefile b/src/alf/makefile
new file mode 100644
index 0000000..d7012d8
--- /dev/null
+++ b/src/alf/makefile
@@ -0,0 +1,43 @@
+#
+# Makefile for alf - Alpha version
+#
+
+#
+# Programs made by this makefile
+#
+PROGS = alfsplit
+
+#
+# Where the wild things are
+#
+SRC = .
+
+#
+# Alpha
+#
+CC = cc
+CFLAGS = -g  -I$(SRC)/../ted
+LD = cc
+LDFLAGS = -g 
+
+
+#
+# Make the programs
+#
+alfsplit: alfsplit.o
+	$(LD) $(LDFLAGS) -o alfsplit alfsplit.o $(LIBS)
+
+2rs: 2rs.o
+	$(LD) $(LDFLAGS) -o 2rs 2rs.o $(LIBS)
+
+
+#
+# Special dependencies
+#
+all: $(PROGS)
+
+clean:
+	/bin/rm -f $(PROGS) *.o *~
+
+%.o : $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
diff --git a/src/alf/makefile-alpha b/src/alf/makefile-alpha
index d7012d8..7df578e 100644
--- a/src/alf/makefile-alpha
+++ b/src/alf/makefile-alpha
@@ -16,9 +16,9 @@ SRC = .
 # Alpha
 #
 CC = cc
-CFLAGS = -g  -I$(SRC)/../ted
+CFLAGS = -g -std1 -ieee_with_inexact -I$(SRC)/../ted
 LD = cc
-LDFLAGS = -g 
+LDFLAGS = -g -non_shared
 
 
 #
diff --git a/src/bap/makefile b/src/bap/makefile
new file mode 100644
index 0000000..593c7ed
--- /dev/null
+++ b/src/bap/makefile
@@ -0,0 +1,580 @@
+# Makefile for staden X programs (Alpha version)
+# ---------------------------------------------------------
+
+# This makefile generates the following staden programs which
+# run under xterm (normal, `N') and those which run directly under X.
+NPROGS=      mep  nip   bap  sap  sip   splitp1 splitp2 splitp3 sethelp
+LPROGS=           nipl     
+XPROGS=     xmep xnip  xbap xsap xsip
+PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
+
+
+
+
+
+
+
+
+#
+# ``Interesting'' suffices that make needs to know about
+#
+.SUFFIXES: .a $(SUFFIXES)
+
+
+#
+# Directories
+#
+SRC = .
+STADENSRC=$(SRC)/../staden
+STADENBIN=$(STADENSRC)
+TEDSRC=$(SRC)/../ted
+TEDBIN=$(TEDSRC)
+OSPSRC=$(SRC)/osp-bits
+OSPBIN=$(OSPSRC)
+MISCSRC=$(SRC)/../Misc
+MISCBIN=$(MISCSRC)
+# Use the ted sources compiled for staden executables
+INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
+
+
+#
+# Compilers and flags
+#
+CC= cc
+CFLAGS= -g $(INCLUDES)
+F77= gfortran
+FFLAGS= -g -fdec -std=legacy -C
+
+#FLIBS= -lfor -lUfor  -lots -lFutil
+FLIBS = -lm -lutil  
+XLIBS= -lXaw -lXt -lXmu -lXext -lX11
+LFLAGS= $(FLIBS)
+XLFLAGS= $(XLIBS) $(FLIBS)
+
+LD = gfortran
+XLD = cc
+LDFLAGS = -g -fdec -std=legacy -L/usr/lib -lgfortran
+
+#
+# Avoid compilation of objects in remote directories
+#
+$(STADENBIN)/%.o : $(STADENSRC)/%.f
+$(STADENBIN)/%.o : $(STADENSRC)/%.c
+$(TEDBIN)/%.o : $(TEDSRC)/%.f
+$(TEDBIN)/%.o : $(TEDSRC)/%.c
+
+#
+# Sequence library handling routines
+#
+SEQLIB=\
+	$(STADENBIN)/seqlibsubs.o
+
+
+
+#
+# The C objects, needed by every X program
+#
+CCORE=\
+	$(STADENBIN)/postscript.o\
+	$(TEDBIN)/Graph.o\
+	$(STADENBIN)/plotLog.o\
+	$(STADENBIN)/help.o\
+	$(STADENBIN)/dialogues.o\
+	$(STADENBIN)/userfacecom.o\
+	$(STADENBIN)/xmenu.o\
+	$(STADENBIN)/locks.o\
+	$(STADENBIN)/mcspec.o\
+	$(STADENBIN)/helpnmenu.o\
+	$(STADENBIN)/FtoC.o
+
+COBJS=\
+	$(STADENBIN)/main.o\
+	$(CCORE)
+
+COBJS2=\
+	xbapmain.o\
+	$(CCORE)
+
+
+#
+# Common objects, needed by every program
+#
+COMMONOBJSB=\
+	$(STADENBIN)/fmain.o\
+	$(STADENBIN)/seeme-aix.o\
+	$(STADENBIN)/nxspec.o\
+	$(STADENBIN)/userface.o\
+	$(STADENBIN)/userfacecom.o\
+	$(STADENBIN)/nxhelpmenu.o\
+	$(STADENBIN)/helpnmenu.o\
+	$(STADENBIN)/FtoC.o\
+	$(STADENBIN)/subs89.a
+
+COMMONOBJS=\
+	$(COMMONOBJSB)\
+	$(STADENBIN)/postscript.o
+
+SCOMMONOBJS=\
+	$(COMMONOBJSB)
+
+XCOMMONOBJS=\
+	$(STADENBIN)/seeme-aix.o\
+	$(STADENBIN)/xspec.o\
+	$(STADENBIN)/subs89.a\
+	$(COBJS)
+
+XCOMMONOBJS2=\
+	$(STADENBIN)/seeme-aix.o\
+	$(STADENBIN)/xspec.o\
+	$(STADENBIN)/subs89.a\
+	$(COBJS2)
+
+
+#
+# Building the programs
+# This should be just a linking phase because all of the object
+# files and library files are generated using implicit rules.
+# We use the fortran compiler to do linking.
+#
+GIP=\
+	$(STADENBIN)/gip.o
+
+GIPOBJS=\
+	$(GIP)\
+	$(SCOMMONOBJS)
+
+gip: $(GIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(GIPOBJS) $(LFLAGS)
+
+
+
+
+MEP=\
+	$(STADENBIN)/mep.o\
+	$(STADENBIN)/mepsub.o\
+	$(STADENBIN)/asubs89.a\
+	$(STADENBIN)/plot92.a
+
+MEPOBJS=\
+	$(MEP)\
+	$(COMMONOBJS)\
+	$(STADENBIN)/pl4010.o
+
+XMEPOBJS=\
+	$(MEP)\
+	$(STADENBIN)/xmepSpec.o\
+	$(XCOMMONOBJS)\
+	$(STADENBIN)/plX.o\
+	$(STADENBIN)/textOutput.o 
+
+mep: $(MEPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(MEPOBJS)  $(LFLAGS)
+
+xmep: $(XMEPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(XMEPOBJS) $(XLFLAGS)
+
+
+
+
+NIP=\
+	$(STADENBIN)/nip.o\
+	$(STADENBIN)/patternn.a\
+	$(STADENBIN)/patternnc.a\
+	$(STADENBIN)/anals89.a\
+	$(STADENBIN)/asubs89.a\
+	$(STADENBIN)/plot92.a $(SEQLIB)
+
+NIPOBJS=\
+	$(NIP)\
+	$(COMMONOBJS)\
+	$(STADENBIN)/pl4010.o
+
+XNIPOBJS=\
+	$(NIP)\
+	$(STADENBIN)/xnipSpec.o\
+	$(XCOMMONOBJS)\
+	$(STADENBIN)/plX.o\
+	$(STADENBIN)/textOutput.o 
+
+nip: $(NIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)
+
+xnip: $(XNIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)
+
+
+
+
+NIPL=\
+	$(STADENBIN)/nipl.o\
+	$(STADENBIN)/patternnc.a\
+	$(STADENBIN)/anals89.a\
+	$(STADENBIN)/asubs89.a\
+	$(SEQLIB)
+
+NIPLOBJS=\
+	$(NIPL)\
+	$(SCOMMONOBJS)
+
+nipl: $(NIPLOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(NIPLOBJS) $(LFLAGS)
+
+
+
+
+PIP=\
+	$(STADENBIN)/pip.o\
+	$(STADENBIN)/analps89.a\
+	$(STADENBIN)/patternp.a\
+	$(STADENBIN)/patternpc.a\
+	$(STADENBIN)/asubs89.a\
+	$(STADENBIN)/plot92.a\
+	$(SEQLIB)
+
+PIPOBJS=\
+	$(PIP)\
+	$(COMMONOBJS)\
+	$(STADENBIN)/pl4010.o
+
+XPIPOBJS=\
+	$(PIP)\
+	$(STADENBIN)/xpipSpec.o\
+	$(XCOMMONOBJS)\
+	$(STADENBIN)/plX.o\
+	$(STADENBIN)/textOutput.o 
+
+pip: $(PIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(PIPOBJS)  $(LFLAGS)
+
+xpip:$(XPIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)
+
+
+
+
+PIPL=\
+	$(STADENBIN)/pipl.o\
+	$(STADENBIN)/patternpc.a\
+	$(STADENBIN)/analps89.a\
+	$(STADENBIN)/asubs89.a\
+	$(SEQLIB)
+
+PIPLOBJS=\
+	$(PIPL)\
+	$(SCOMMONOBJS)
+
+pipl: $(PIPLOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(PIPLOBJS)  $(LFLAGS)
+
+
+
+#
+# Trace manager objects
+#
+STDTEDFILES=\
+	$(TEDBIN)/seq.o\
+	$(TEDBIN)/seqIOABI.o\
+	$(TEDBIN)/seqIOALF.o\
+	$(TEDBIN)/seqIOSCF.o\
+	$(TEDBIN)/seqIOPlain.o\
+	$(TEDBIN)/opp.o\
+	$(TEDBIN)/fpoint.o\
+	$(TEDBIN)/mach-io.o
+
+TMANOBJS=\
+	$(STADENBIN)/tman_main.o\
+	$(STADENBIN)/tman_display.o\
+	$(STADENBIN)/tman_traceDisplay.o\
+	$(STADENBIN)/tman_basesDisplay.o\
+	$(STADENBIN)/tman_context.o\
+	$(STADENBIN)/tman_gadgets.o\
+	$(STDTEDFILES)
+
+OSPOBJS=\
+	$(OSPBIN)/analysis.o\
+	$(OSPBIN)/our_allo.o\
+	$(OSPBIN)/paramIOX.o\
+	$(OSPBIN)/paramIO.o\
+	$(OSPBIN)/get_scores.o\
+	$(OSPBIN)/utils.o\
+	mess.o\
+	$(GNULIB)
+
+XHACK=\
+	$(STADENBIN)/SmeLine.o
+
+EDITOR=\
+	$(XHACK)\
+	$(STADENBIN)/xsapConEdit.o\
+	contigEditor.o\
+	edUtils.o\
+	$(STADENBIN)/undo.o\
+	$(STADENBIN)/Sheet.o\
+	$(STADENBIN)/select.o\
+	$(STADENBIN)/extend.o\
+	$(STADENBIN)/searchUtils.o\
+	edMenu.o\
+	oligo.o\
+	oligocom.o\
+	subclone.o\
+	myparams.o\
+	$(STADENBIN)/trans.o\
+	$(MISCBIN)/misc.a
+
+TAGEDITOR=\
+	$(STADENBIN)/tagEditor.o\
+	$(STADENBIN)/tagdbparse.o\
+	tagU2.o\
+	$(STADENBIN)/tagU1.o
+
+BAP=\
+	bap.o\
+	dbsysnew.o\
+	dbsyscommon.o\
+	actf.o\
+	dstrand.o\
+	oligo_sel.o\
+	llin.o\
+	guk.o\
+	$(STADENBIN)/asubs89.a\
+	$(STADENBIN)/plot92.a
+
+BAPOBJS=\
+	$(BAP)\
+	$(COMMONOBJS)\
+	$(STADENBIN)/pl4010.o\
+	$(STADENBIN)/conEdit.o\
+	tagU2.o\
+	$(OSPBIN)/analysis.o\
+	$(OSPBIN)/our_allo.o\
+	$(OSPBIN)/get_scores.o\
+	$(OSPBIN)/utils.o\
+	mess.o\
+	baponly.o\
+	oligocom.o
+
+XBAPOBJS=\
+	$(BAP)\
+	$(XCOMMONOBJS2)\
+	$(STADENBIN)/plX.o\
+	$(STADENBIN)/textOutput.o\
+	$(EDITOR)\
+	$(TMANOBJS)\
+	$(TAGEDITOR)\
+	$(OSPOBJS)
+
+bap:	$(BAPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(BAPOBJS) $(LFLAGS)
+
+xbap:	$(XBAPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(XBAPOBJS) $(XLFLAGS)
+
+SAP=\
+	sap.o\
+	dbsyscommon.o\
+	dbsysold.o\
+	$(STADENBIN)/asubs89.a\
+	$(STADENBIN)/plot92.a
+
+SAPOBJS=\
+	$(SAP)\
+	$(COMMONOBJS)\
+	$(STADENBIN)/pl4010.o
+
+XSAPOBJS=\
+	$(SAP)\
+	$(STADENBIN)/xsapSpec.o\
+	$(XCOMMONOBJS)\
+	$(STADENBIN)/plX.o\
+	$(STADENBIN)/textOutput.o 
+
+sap: $(SAPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)
+
+xsap: $(XSAPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)
+
+
+
+
+SAPF=\
+	$(STADENBIN)/sapf.o\
+	$(STADENBIN)/dbsyscommon.o\
+	$(STADENBIN)/dbsysold.o\
+	$(STADENBIN)/asubs89.a\
+	$(STADENBIN)/plot92.a
+
+SAPFOBJS=\
+	$(SAPF)\
+	$(STADENBIN)/sapmen.o\
+	$(COMMONOBJS)\
+	$(STADENBIN)/pl4010.o
+
+sapf: $(SAPFOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)
+
+
+
+
+
+
+SIP=\
+	$(STADENBIN)/sip.o\
+	$(STADENBIN)/dias89.a\
+	$(STADENBIN)/plot92.a\
+	$(SEQLIB)
+
+SIPOBJS=\
+	$(SIP)\
+	$(COMMONOBJS)\
+	$(STADENBIN)/pl4010.o
+
+XSIPOBJS=\
+	$(SIP)\
+	$(STADENBIN)/xsipSpec.o\
+	$(XCOMMONOBJS)\
+	$(STADENBIN)/plX.o\
+	$(STADENBIN)/textOutput.o 
+
+sip: $(SIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)
+
+xsip: $(XSIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)
+
+
+
+
+SIPL=\
+	$(STADENBIN)/sipl.o\
+	$(STADENBIN)/dias89.a\
+	$(SEQLIB)
+
+SIPLOBJS=\
+	$(SIPL)\
+	$(SCOMMONOBJS)
+
+sipl: $(SIPLOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)
+
+
+
+
+SETHELP=\
+	$(STADENBIN)/sethelp.o
+
+SETHELPOBJS=\
+	$(SETHELP)\
+	$(SCOMMONOBJS)
+
+sethelp: $(SETHELPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)
+
+
+
+
+SPLITP1=\
+	$(STADENBIN)/splitp1.o
+SPLITP1OBJS=\
+	$(SPLITP1)\
+	$(SCOMMONOBJS)
+
+splitp1: $(SPLITP1OBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)
+
+
+
+
+SPLITP2=\
+	$(STADENBIN)/splitp2.o
+SPLITP2OBJS=\
+	$(SPLITP2)\
+	$(SCOMMONOBJS)
+
+splitp2: $(SPLITP2OBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)
+
+
+
+
+
+SPLITP3=\
+	$(STADENBIN)/splitp3.o
+SPLITP3OBJS=\
+	$(SPLITP3)\
+	$(SCOMMONOBJS)
+
+splitp3: $(SPLITP3OBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)
+
+
+
+
+
+#
+# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
+# 
+%.o: $(SRC)/%.f
+	$(F77) $(FFLAGS) -c $<
+
+
+#
+# Files requiring simple C compilation (thing.c -> thing.o)
+# 
+%.o: %.c
+	$(CC) $(CFLAGS) -c $<
+%.o: $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+
+
+
+#
+# The UNIX library (archive) mechanism is fairly weak so the following
+# procedure is used to generate libraries.
+#   * split the source file up into files which each contain
+#     a single function or subroutine
+#   * compile each of those files
+#   * insert the object files individually into the library
+# Each library is built by using a temporary directory.
+# The fortran compilations must be done sequentially in order to
+# 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 $$TMPDIR
+
+
+#%.a: $(SRC)/%.f
+#	$(F77) $(FFLAGS) -c *.f; 
+#	ar rcv $$BINDIR/$@ *.o; 
+
+
+
+all: $(NPROGS) $(XPROGS) $(LPROGS)
+
+nprogs: $(NPROGS)
+
+xprogs: $(XPROGS)
+
+lprogs: $(LPROGS)
+
+clean:
+	rm -f $(PROGS) *.o *.a *~
diff --git a/src/bap/makefile-alpha b/src/bap/makefile-alpha
index 593c7ed..7cf135b 100644
--- a/src/bap/makefile-alpha
+++ b/src/bap/makefile-alpha
@@ -3,9 +3,9 @@
 
 # This makefile generates the following staden programs which
 # run under xterm (normal, `N') and those which run directly under X.
-NPROGS=      mep  nip   bap  sap  sip   splitp1 splitp2 splitp3 sethelp
-LPROGS=           nipl     
-XPROGS=     xmep xnip  xbap xsap xsip
+NPROGS=      mep  nip   pip   bap  sap  sip   splitp1 splitp2 splitp3 sethelp convert_project
+LPROGS=           nipl  pip             sipl
+XPROGS=     xmep xnip  xpip  xbap xsap xsip
 PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
 
 
@@ -26,13 +26,13 @@ PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
 #
 SRC = .
 STADENSRC=$(SRC)/../staden
-STADENBIN=$(STADENSRC)
+STADENBIN=$(STADENSRC)/alpha-binaries
 TEDSRC=$(SRC)/../ted
-TEDBIN=$(TEDSRC)
+TEDBIN=$(STADENBIN)
 OSPSRC=$(SRC)/osp-bits
-OSPBIN=$(OSPSRC)
+OSPBIN=$(OSPSRC)/alpha-binaries
 MISCSRC=$(SRC)/../Misc
-MISCBIN=$(MISCSRC)
+MISCBIN=$(MISCSRC)/alpha-binaries
 # Use the ted sources compiled for staden executables
 INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
 
@@ -41,19 +41,18 @@ INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
 # Compilers and flags
 #
 CC= cc
-CFLAGS= -g $(INCLUDES)
-F77= gfortran
-FFLAGS= -g -fdec -std=legacy -C
+CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES)
+F77= f77
+FFLAGS= -g -C
 
-#FLIBS= -lfor -lUfor  -lots -lFutil
-FLIBS = -lm -lutil  
+FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil -ldnet_stub
 XLIBS= -lXaw -lXt -lXmu -lXext -lX11
 LFLAGS= $(FLIBS)
 XLFLAGS= $(XLIBS) $(FLIBS)
 
-LD = gfortran
+LD = f77
 XLD = cc
-LDFLAGS = -g -fdec -std=legacy -L/usr/lib -lgfortran
+LDFLAGS = -g -non_shared
 
 #
 # Avoid compilation of objects in remote directories
@@ -76,7 +75,7 @@ SEQLIB=\
 #
 CCORE=\
 	$(STADENBIN)/postscript.o\
-	$(TEDBIN)/Graph.o\
+	$(STADENBIN)/Graph.o\
 	$(STADENBIN)/plotLog.o\
 	$(STADENBIN)/help.o\
 	$(STADENBIN)/dialogues.o\
@@ -101,7 +100,7 @@ COBJS2=\
 #
 COMMONOBJSB=\
 	$(STADENBIN)/fmain.o\
-	$(STADENBIN)/seeme-aix.o\
+	$(STADENBIN)/seeme-dec.o\
 	$(STADENBIN)/nxspec.o\
 	$(STADENBIN)/userface.o\
 	$(STADENBIN)/userfacecom.o\
@@ -118,13 +117,13 @@ SCOMMONOBJS=\
 	$(COMMONOBJSB)
 
 XCOMMONOBJS=\
-	$(STADENBIN)/seeme-aix.o\
+	$(STADENBIN)/seeme-dec.o\
 	$(STADENBIN)/xspec.o\
 	$(STADENBIN)/subs89.a\
 	$(COBJS)
 
 XCOMMONOBJS2=\
-	$(STADENBIN)/seeme-aix.o\
+	$(STADENBIN)/seeme-dec.o\
 	$(STADENBIN)/xspec.o\
 	$(STADENBIN)/subs89.a\
 	$(COBJS2)
@@ -367,7 +366,7 @@ bap:	$(BAPOBJS)
 	$(LD) $(LDFLAGS) -o $@ $(BAPOBJS) $(LFLAGS)
 
 xbap:	$(XBAPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(XBAPOBJS) $(XLFLAGS)
+	$(XLD) $(LDFLAGS) -o $@ $(XBAPOBJS) $(XLFLAGS)
 
 SAP=\
 	sap.o\
@@ -541,30 +540,28 @@ 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
+
 
 
-#%.a: $(SRC)/%.f
-#	$(F77) $(FFLAGS) -c *.f; 
-#	ar rcv $$BINDIR/$@ *.o; 
 
 
 
diff --git a/src/convert/makefile b/src/convert/makefile
new file mode 100644
index 0000000..0a49ee8
--- /dev/null
+++ b/src/convert/makefile
@@ -0,0 +1,45 @@
+#
+# Makefile for convert (Alpha version)
+#
+
+SRC = .
+MISCSRC=$(SRC)/../Misc
+MISCBIN=$(MISCSRC)
+
+CC = cc
+CFLAGS = -g -I$(MISCSRC)
+LD = cc
+LDFLAGS = -g
+LIBS = $(MISCBIN)/misc.a
+
+#
+# Programs made by this makefile
+#
+PROGS = convert
+
+all : $(PROGS)
+
+#
+# Where the wild things are
+#
+
+OBJS = \
+	list.o \
+	main.o \
+	dapIO.o \
+	dapDB.o \
+	bapIO.o \
+	bapDB.o \
+	process.o \
+	flat_sd.o
+
+convert: $(OBJS)
+	$(LD) $(LDFLAGS) -o convert $(OBJS) $(LIBS) $(LDFLAGS)
+#
+# Special dependencies
+#
+%.o:$(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+clean :
+	/bin/rm -f $(PROGS) $(OBJS) *~
diff --git a/src/convert/makefile-alpha b/src/convert/makefile-alpha
index 0a49ee8..30cf237 100644
--- a/src/convert/makefile-alpha
+++ b/src/convert/makefile-alpha
@@ -4,12 +4,12 @@
 
 SRC = .
 MISCSRC=$(SRC)/../Misc
-MISCBIN=$(MISCSRC)
+MISCBIN=$(MISCSRC)/alpha-binaries
 
 CC = cc
-CFLAGS = -g -I$(MISCSRC)
+CFLAGS = -g -std1 -ieee_with_inexact -I$(MISCSRC)
 LD = cc
-LDFLAGS = -g
+LDFLAGS = -g -non_shared
 LIBS = $(MISCBIN)/misc.a
 
 #
diff --git a/src/cop/makefile b/src/cop/makefile
new file mode 100644
index 0000000..7d7d060
--- /dev/null
+++ b/src/cop/makefile
@@ -0,0 +1,114 @@
+#
+# Makefile for COP (Check Out Project) - Alpha version
+#
+
+#
+# Programs made by this makefile
+#
+PROGS = cop cop-bap
+all: $(PROGS)
+#
+# Where the wild things are
+#
+SRC = .
+TEDSRC = $(SRC)/../ted
+MISCSRC = $(SRC)/../Misc
+MISCBIN = $(MISCSRC)
+CONVERTSRC = $(SRC)/../convert
+INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC)
+
+#
+# Alpha
+#
+CC = cc
+CFLAGS = -g $(INCLUDES)
+LD = cc
+LDFLAGS = -g 
+LIBFLAGS = 
+
+#
+# Main and miscellaneous routines
+#
+COPOBJ = \
+	cop.o
+
+COPBAPOBJ = \
+	cop-bap.o
+
+LIBS = \
+	$(MISCBIN)/misc.a
+
+#
+# For reading in xdap database
+#
+XDAPIO = \
+	dapIO.o
+
+XBAPIO = \
+	bapIO.o
+
+#
+# For reading in trace files
+#
+TRACES = \
+	getSeq.o \
+	seqIOABI.o \
+	seqIOALF.o \
+	seqIOSCF.o \
+	seqIOPlain.o \
+	opp.o \
+	seq.o \
+	fpoint.o\
+	mach-io.o
+
+#
+# For aligning sequences
+#
+ALIGN = \
+	llin.o
+
+#
+# The whole lot
+#
+OBJ = \
+	$(COPOBJ) \
+	$(XDAPIO) \
+	$(TRACES) \
+	$(ALIGN)
+
+OBJBAP = \
+	$(COPBAPOBJ) \
+	$(XBAPIO) \
+	$(TRACES) \
+	$(ALIGN)
+
+
+#
+# Cop
+#
+cop : $(OBJ)
+	$(LD) $(LDFLAGS) -o cop $(OBJ) $(LIBS) $(LIBFLAGS)
+
+cop-bap : $(OBJBAP)
+	$(LD) $(LDFLAGS) -o cop-bap $(OBJBAP) $(LIBS) $(LIBFLAGS)
+
+
+
+#
+# Special dependencies
+#
+
+all: $(PROGS)
+
+clean:
+	/bin/rm -f $(OBJ) $(PROGS) *~
+
+cop-bap.o: $(SRC)/cop.c
+	$(CC) -DBAP_VERSION $(CFLAGS) -o cop-bap.o -c $(SRC)/cop.c
+
+%.o: $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+%.o: $(TEDSRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
diff --git a/src/cop/makefile-alpha b/src/cop/makefile-alpha
index 7d7d060..26c2255 100644
--- a/src/cop/makefile-alpha
+++ b/src/cop/makefile-alpha
@@ -6,14 +6,14 @@
 # Programs made by this makefile
 #
 PROGS = cop cop-bap
-all: $(PROGS)
+
 #
 # Where the wild things are
 #
 SRC = .
 TEDSRC = $(SRC)/../ted
 MISCSRC = $(SRC)/../Misc
-MISCBIN = $(MISCSRC)
+MISCBIN = $(MISCSRC)/alpha-binaries
 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 $(INCLUDES)
+CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES)
 LD = cc
-LDFLAGS = -g 
+LDFLAGS = -g -non_shared
 LIBFLAGS = 
 
 #
diff --git a/src/expGetSeq/makefile b/src/expGetSeq/makefile
new file mode 100644
index 0000000..e1fb49b
--- /dev/null
+++ b/src/expGetSeq/makefile
@@ -0,0 +1,93 @@
+#
+# Makefile for expGetSeq - Alpha version
+#
+
+#
+# Turning on the AUTO_CLIP switch allows ted to automatically
+# select a left (using the -enzyme option or the .enzyme in the
+# Xted file) and right cutoff on your sequence (using 2 out of
+# 5 N's)
+#
+# Turning on the SAVE_EDITS switch allows the user to maintain
+# copies of their edits, i.e. when you open up ted on a file
+# that you have already edited, the old edits show up in the
+# ted edit window.  The user may also call up any of their
+# past editing sessions.  
+#
+# Turning on the DEF_OUT  switch makes
+# trace_name.seq the default output file name
+#
+# Turning on the QUAL_CODE switch enables LaDeana's trace quality
+# clipping code.
+#
+# Turning on the QUAL_CHECK switch (at the same time as QUAL_CODE)
+# enables the overall trace quality check.
+#
+#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS  -DQUAL_CODE -DQUAL_CHECK
+SWITCHES = -DAUTO_CLIP -DQUAL_CODE
+
+#
+# Programs made by this makefile
+#
+PROGS = expGetSeq
+
+#
+# Where the wild things are
+#
+SRC = .
+TEDSRC = $(SRC)/../newted
+INCLUDES = -I/usr/include/mit -I$(SRC) -I$(TEDSRC)
+
+#
+# Compiler - debug on
+#
+CC= cc
+CFLAGS= -g  $(SWITCHES) $(INCLUDES)
+LD= cc
+LDFLAGS= -g
+
+
+#
+# Object files
+#
+OBJS=\
+	getMCH.o\
+	seq.o\
+	seqIOPlain.o\
+	seqIOABI.o\
+	seqIOEdit.o\
+	seqIOALF.o\
+	seqIOSCF.o\
+	opp.o\
+	fpoint.o\
+	match.o\
+	mach-io.o\
+	seqRead.o\
+	traceType.o
+
+
+#
+# Linking
+#
+expGetSeq: $(OBJS)
+	$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS)
+
+#
+# Files requiring simple C compilation (thing.c -> thing.o)
+# 
+%.o : %.c
+	$(CC) $(CFLAGS) -c $<
+%.o : $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+%.o : $(TEDSRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+
+#
+# Special dependencies
+#
+clean:
+	rm -f $(PROGS) $(OBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
+
+all: $(PROGS)
+
diff --git a/src/expGetSeq/makefile-alpha b/src/expGetSeq/makefile-alpha
index e1fb49b..af3252c 100644
--- a/src/expGetSeq/makefile-alpha
+++ b/src/expGetSeq/makefile-alpha
@@ -42,9 +42,9 @@ INCLUDES = -I/usr/include/mit -I$(SRC) -I$(TEDSRC)
 # Compiler - debug on
 #
 CC= cc
-CFLAGS= -g  $(SWITCHES) $(INCLUDES)
+CFLAGS= -g -ieee_with_inexact $(SWITCHES) $(INCLUDES)
 LD= cc
-LDFLAGS= -g
+LDFLAGS= -g -non_shared
 
 
 #
diff --git a/src/frog/makefile b/src/frog/makefile
new file mode 100644
index 0000000..4133818
--- /dev/null
+++ b/src/frog/makefile
@@ -0,0 +1,35 @@
+CC = cc
+CFLAGS = -g 
+LD = cc
+LDFLAGS = -g
+LIBFLAGS =
+
+SRC = .
+PROGS = frog toad
+all: $(PROGS)
+
+FROGOBJ =\
+	frog.o\
+	mach-io.o
+
+frog : $(FROGOBJ)
+	$(LD) $(LDFLAGS) -o frog $(FROGOBJ) $(LIBFLAGS)
+
+
+TOADOBJ =\
+	toad.o\
+	scfIO.o\
+	mach-io.o
+
+toad : $(TOADOBJ)
+	$(LD) $(LDFLAGS) -o toad $(TOADOBJ) $(LIBFLAGS)
+
+
+#
+# Specials
+#
+%.o:$(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+clean:
+	/bin/rm -f $(PROGS) $(FROGOBJ)
diff --git a/src/frog/makefile-alpha b/src/frog/makefile-alpha
index 4133818..3d8bef9 100644
--- a/src/frog/makefile-alpha
+++ b/src/frog/makefile-alpha
@@ -1,7 +1,7 @@
 CC = cc
-CFLAGS = -g 
+CFLAGS = -g -std1 -ieee_with_inexact
 LD = cc
-LDFLAGS = -g
+LDFLAGS = -g -non_shared
 LIBFLAGS =
 
 SRC = .
diff --git a/src/getMCH/makefile b/src/getMCH/makefile
new file mode 100644
index 0000000..ffb6dee
--- /dev/null
+++ b/src/getMCH/makefile
@@ -0,0 +1,86 @@
+#
+# Makefile for getMCH - Alpha version
+#
+
+#
+#Turning on the AUTO_CLIP switch allows ted to automatically
+#select a left (using the -enzyme option or the .enzyme in the
+#Xted file) and right cutoff on your sequence (using 2 out of
+#5 N's)
+#
+# Turning on the SAVE_EDITS switch allows the user to maintain
+# copies of their edits, i.e. when you open up ted on a file
+# that you have already edited, the old edits show up in the
+# ted edit window.  The user may also call up any of their
+# past editing sessions.  
+#
+#Turning on the DEF_OUT  switch makes
+# trace_name.seq the default output file name
+#
+#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS
+
+#
+# Programs made by this makefile
+#
+PROGS = getMCH trace2seq
+all: $(PROGS)
+#
+# Where the wild things are
+#
+SRC = .
+TEDSRC = $(SRC)/../ted
+INCLUDES = -I$(SRC) -I$(TEDSRC)
+
+#
+# Compiler - debug on
+#
+CC= cc
+CFLAGS= -g $(SWITCHES) $(INCLUDES)
+LD= cc
+LDFLAGS= -g
+LIBFLAGS =
+
+
+#
+# Object files
+#
+OBJS=\
+	getMCH.o\
+	seq.o\
+	seqIOPlain.o\
+	seqIOABI.o\
+	seqIOEdit.o\
+	seqIOALF.o\
+	seqIOSCF.o\
+	seqOutput.o\
+	opp.o\
+	fpoint.o\
+	match.o\
+	mach-io.o
+
+
+#
+# Linking
+#
+trace2seq getMCH: $(OBJS)
+	$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS) $(LIBFLAGS)
+
+#
+# Files requiring simple C compilation (thing.c -> thing.o)
+# 
+%.o : %.c
+	$(CC) $(CFLAGS) -c $<
+%.o : $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+%.o : $(TEDSRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+
+#
+# Special dependencies
+#
+clean:
+	rm -f $(PROGS) $(OBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
+
+all: $(PROGS)
+
diff --git a/src/getMCH/makefile-alpha b/src/getMCH/makefile-alpha
index ffb6dee..c8dcb14 100644
--- a/src/getMCH/makefile-alpha
+++ b/src/getMCH/makefile-alpha
@@ -23,7 +23,7 @@
 # Programs made by this makefile
 #
 PROGS = getMCH trace2seq
-all: $(PROGS)
+
 #
 # Where the wild things are
 #
@@ -35,9 +35,9 @@ INCLUDES = -I$(SRC) -I$(TEDSRC)
 # Compiler - debug on
 #
 CC= cc
-CFLAGS= -g $(SWITCHES) $(INCLUDES)
+CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
 LD= cc
-LDFLAGS= -g
+LDFLAGS= -g -non_shared
 LIBFLAGS =
 
 
diff --git a/src/indexseqlibs/makefile b/src/indexseqlibs/makefile
new file mode 100644
index 0000000..29f98f5
--- /dev/null
+++ b/src/indexseqlibs/makefile
@@ -0,0 +1,172 @@
+#
+# indexseqlibs - Alpha version
+#
+
+all: $(PROGS)
+
+#
+# Programs need making
+#
+PROGS = \
+	addnl \
+	genbentryname1 \
+	entryname2 \
+	access4 \
+	access2 \
+	genbaccess1 \
+	title2 \
+	genbtitle1 \
+	emblentryname1 \
+	emblaccess1 \
+	embltitle1 \
+	pirentryname1 \
+	piraccess1 \
+	piraccess2 \
+	pirtitle1 \
+	pirtitle2 \
+	excludewords \
+	emblfreetext \
+	genbfreetext \
+	pirfreetext \
+	freetext2 \
+	freetext4 \
+	emblauthor \
+	genbauthor \
+	pirauthor \
+	hitNtrg \
+	division
+
+#
+# Where the wild things are
+#
+SRC = .
+
+#
+# Alpha
+#
+CC = cc
+CFLAGS = -g
+LD = cc
+LDFLAGS = -g
+
+#
+# Shared objects
+#
+OBJS = \
+	cdromheader.o \
+	mach-io.o
+
+#
+# Dependencies for programs
+#
+addnl : addnl.o
+	$(LD) $(LDFLAGS) -o $@ addnl.o
+
+genbentryname1 : genbentryname1.o
+	$(LD) $(LDFLAGS) -o $@ genbentryname1.o
+
+entryname2 : entryname2.o $(OBJS)
+	$(LD) $(LDFLAGS) -o $@ entryname2.o $(OBJS)
+
+access4 : access4.o $(OBJS)
+	$(LD) $(LDFLAGS) -o $@ access4.o $(OBJS)
+
+access2 : access2.o
+	$(LD) $(LDFLAGS) -o $@ access2.o
+
+genbaccess1 : genbaccess1.o
+	$(LD) $(LDFLAGS) -o $@ genbaccess1.o
+
+title2 : title2.o $(OBJS)
+	$(LD) $(LDFLAGS) -o $@ title2.o $(OBJS)
+
+genbtitle1 : genbtitle1.o
+	$(LD) $(LDFLAGS) -o $@ genbtitle1.o
+
+emblentryname1 : emblentryname1.o
+	$(LD) $(LDFLAGS) -o $@ emblentryname1.o
+
+emblaccess1 : emblaccess1.o
+	$(LD) $(LDFLAGS) -o $@ emblaccess1.o
+
+embltitle1 : embltitle1.o
+	$(LD) $(LDFLAGS) -o $@ embltitle1.o
+
+pirentryname1 : pirentryname1.o
+	$(LD) $(LDFLAGS) -o $@ pirentryname1.o
+
+piraccess1 : piraccess1.o
+	$(LD) $(LDFLAGS) -o $@ piraccess1.o
+
+piraccess2 : piraccess2.o
+	$(LD) $(LDFLAGS) -o $@ piraccess2.o
+
+pirtitle1 : pirtitle1.o
+	$(LD) $(LDFLAGS) -o $@ pirtitle1.o
+
+pirtitle2 : pirtitle2.o
+	$(LD) $(LDFLAGS) -o $@ pirtitle2.o
+
+excludewords : excludewords.o
+	$(LD) $(LDFLAGS) -o $@ excludewords.o
+
+emblfreetext.o: $(SRC)/freetext.c
+	$(CC) $(CFLAGS) -DEMBL -c -o $@ $<
+emblfreetext : emblfreetext.o
+	$(LD) $(LDFLAGS) -o $@ emblfreetext.o
+
+genbfreetext.o: $(SRC)/freetext.c
+	$(CC) $(CFLAGS) -DGENBANK -c -o $@ $<
+genbfreetext : genbfreetext.o
+	$(LD) $(LDFLAGS) -o $@ genbfreetext.o
+
+pirfreetext.o: $(SRC)/freetext.c
+	$(CC) $(CFLAGS) -DPIR -c -o $@ $<
+pirfreetext : pirfreetext.o
+	$(LD) $(LDFLAGS) -o $@ pirfreetext.o
+
+freetext2 : freetext2.o
+	$(LD) $(LDFLAGS) -o $@ freetext2.o
+
+freetext4 : freetext4.o $(OBJS)
+	$(LD) $(LDFLAGS) -o $@ freetext4.o $(OBJS)
+
+emblauthor.o : $(SRC)/author.c
+	$(CC) $(CFLAGS) -DEMBL -c -o $@ $<
+emblauthor : emblauthor.o
+	$(LD) $(LDFLAGS) -o $@ emblauthor.o
+
+genbauthor.o : $(SRC)/author.c
+	$(CC) $(CFLAGS) -DGENBANK -c -o $@ $<
+genbauthor : genbauthor.o
+	$(LD) $(LDFLAGS) -o $@ genbauthor.o
+
+pirauthor.o : $(SRC)/author.c
+	$(CC) $(CFLAGS) -DPIR -c -o $@ $<
+pirauthor : pirauthor.o
+	$(LD) $(LDFLAGS) -o $@ pirauthor.o
+
+hitNtrg : hitNtrg.o $(OBJS)
+	$(LD) $(LDFLAGS) -o $@ hitNtrg.o $(OBJS)
+
+division : division.o $(OBJS)
+	$(LD) $(LDFLAGS) -o $@ division.o $(OBJS)
+
+
+
+
+#
+# Special dependencies
+#
+%.o : $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+
+
+
+all : $(PROGS)
+
+clean :
+	/bin/rm -f $(PROGS) *.o *~
+
+
diff --git a/src/indexseqlibs/makefile-alpha b/src/indexseqlibs/makefile-alpha
index 29f98f5..f150f63 100644
--- a/src/indexseqlibs/makefile-alpha
+++ b/src/indexseqlibs/makefile-alpha
@@ -2,7 +2,6 @@
 # indexseqlibs - Alpha version
 #
 
-all: $(PROGS)
 
 #
 # Programs need making
@@ -45,9 +44,9 @@ SRC = .
 # Alpha
 #
 CC = cc
-CFLAGS = -g
+CFLAGS = -g -std1 -ieee_with_inexact
 LD = cc
-LDFLAGS = -g
+LDFLAGS = -g -non_shared
 
 #
 # Shared objects
diff --git a/src/newted/makefile b/src/newted/makefile
new file mode 100644
index 0000000..faab788
--- /dev/null
+++ b/src/newted/makefile
@@ -0,0 +1,117 @@
+#
+# Makefile for ted (trace editor) - Alpha fork
+#
+
+#
+# Turning on the AUTO_CLIP switch allows ted to automatically
+# select a left (using the -enzyme option or the .enzyme in the
+# Xted file) and right cutoff on your sequence (using 2 out of
+# 5 N's)
+#
+# Turning on the SAVE_EDITS switch allows the user to maintain
+# copies of their edits, i.e. when you open up ted on a file
+# that you have already edited, the old edits show up in the
+# ted edit window.  The user may also call up any of their
+# past editing sessions.  
+#
+# Turning on the DEF_OUT  switch makes
+# trace_name.seq the default output file name
+#
+# Turning on the QUAL_CODE switch enables LaDeana's trace quality
+# clipping code.
+#
+# Turning on the QUAL_CHECK switch (at the same time as QUAL_CODE)
+# enables the overall trace quality check.
+#
+#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS  -DQUAL_CODE -DQUAL_CHECK
+SWITCHES = -DAUTO_CLIP -DQUAL_CODE -DQUAL_CHECK
+
+
+#
+# Programs made by this makefile
+#
+PROGS = ted autoted
+
+#
+# Where the wild things are
+#
+SRC = .
+
+#
+# Compiler - debug on
+#
+CC= cc
+INCLUDES = -I$(SRC)
+CFLAGS= -g  $(SWITCHES) $(INCLUDES)
+LIBS= -lXaw -lXt -lXmu -lXext -lX11 
+#
+LD= cc
+LDFLAGS= -g 
+
+#
+# Object files
+#
+TEDOBJS=\
+	ted.o\
+	dialogues.o\
+	seq.o\
+	seqIOPlain.o\
+	seqIOABI.o\
+	help.o\
+	display.o\
+	traceDisplay.o\
+	basesDisplay.o\
+	Graph.o\
+	seqIOEdit.o\
+	seqIOALF.o\
+	seqIOSCF.o\
+	seqOutput.o\
+	opp.o\
+	info.o\
+	fpoint.o\
+	mach-io.o\
+	seqRead.o\
+	traceType.o\
+	match.o
+
+AUTOTEDOBJS=\
+	autoted.o\
+	seq.o\
+	seqIOPlain.o\
+	seqIOABI.o\
+	seqIOEdit.o\
+	seqIOALF.o\
+	seqIOSCF.o\
+	seqOutput.o\
+	opp.o\
+	traceType.o\
+	fpoint.o\
+	mach-io.o\
+	match.o\
+	seqRead.o
+
+
+
+#
+# Linking
+#
+ted: $(TEDOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(TEDOBJS) $(LIBS)
+autoted: $(AUTOTEDOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(AUTOTEDOBJS) $(LIBS)
+
+#
+# Files requiring simple C compilation (thing.c -> thing.o)
+# 
+%.o : $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+
+#
+# Special dependencies
+#
+clean:
+	rm -f ted $(TEDOBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
+
+all: $(PROGS)
+
diff --git a/src/newted/makefile-alpha b/src/newted/makefile-alpha
index faab788..e6707b2 100644
--- a/src/newted/makefile-alpha
+++ b/src/newted/makefile-alpha
@@ -42,11 +42,11 @@ SRC = .
 #
 CC= cc
 INCLUDES = -I$(SRC)
-CFLAGS= -g  $(SWITCHES) $(INCLUDES)
-LIBS= -lXaw -lXt -lXmu -lXext -lX11 
+CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
+LIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub
 #
 LD= cc
-LDFLAGS= -g 
+LDFLAGS= -g -non_shared
 
 #
 # Object files
diff --git a/src/scf/makefile b/src/scf/makefile
new file mode 100644
index 0000000..627ce01
--- /dev/null
+++ b/src/scf/makefile
@@ -0,0 +1,67 @@
+#
+# getMCH - Alpha version
+#
+
+#
+# Programs made by this makefile
+#
+PROGS = makeSCF
+
+#
+# SWITCHES - see ted makefile
+#
+#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS
+
+#
+# Where the wild things are
+#
+SRC = .
+TEDSRC = $(SRC)/../ted
+
+#
+# alpha
+#
+CC= cc
+CFLAGS= -g  $(SWITCHES) -I$(TEDSRC)
+LD= cc
+LDFLAGS= -g
+LIBFLAGS =
+
+%.o : $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+%.o : $(TEDSRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+#
+# Object files
+#
+OBJS=\
+	makeSCF.o\
+	writeSCF.o\
+	seq.o\
+	seqIOPlain.o\
+	seqIOABI.o\
+	seqIOEdit.o\
+	seqIOALF.o\
+	seqIOSCF.o\
+	seqOutput.o\
+	opp.o\
+	fpoint.o\
+	match.o\
+	mach-io.o
+
+
+#
+# Linking
+#
+makeSCF: $(OBJS)
+	$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS) $(LIBFLAGS)
+
+#
+# Special dependencies
+#
+all: $(PROGS) 
+
+clean:
+	/bin/rm -f $(OBJS) $(PROGS) *~
diff --git a/src/scf/makefile-alpha b/src/scf/makefile-alpha
index 627ce01..331c209 100644
--- a/src/scf/makefile-alpha
+++ b/src/scf/makefile-alpha
@@ -22,9 +22,9 @@ TEDSRC = $(SRC)/../ted
 # alpha
 #
 CC= cc
-CFLAGS= -g  $(SWITCHES) -I$(TEDSRC)
+CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) -I$(TEDSRC)
 LD= cc
-LDFLAGS= -g
+LDFLAGS= -g -non_shared
 LIBFLAGS =
 
 %.o : $(SRC)/%.c
diff --git a/src/staden/makefile b/src/staden/makefile
new file mode 100644
index 0000000..2b98054
--- /dev/null
+++ b/src/staden/makefile
@@ -0,0 +1,603 @@
+# Makefile for staden X programs (Alpha OSF/1.2 version)
+# ------------------------------------------------------
+
+# This makefile generates the following staden programs which
+# run under xterm (normal, `N') and those which run directly under X.
+NPROGS=      mep  nip   pip   dap  sap  sip   splitp1 splitp2 splitp3 gip sethelp convert_project rep lip sapf nipf vep
+LPROGS=           nipl  pipl            sipl
+XPROGS=     xmep xnip  xpip  xdap xsap xsip
+PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
+
+#
+# ``Interesting'' suffices that make needs to know about
+#
+.SUFFIXES: .a $(SUFFIXES)
+
+#
+# Where the wild things are
+#
+SRC=.
+TEDSRC=$(SRC)/../ted
+MISCSRC=$(SRC)/../Misc
+MISCBIN=$(MISCSRC)
+INCLUDES= -I$(SRC) -I$(TEDSRC) -I$(MISCSRC)
+
+#
+# Compilers and flags
+#
+CC= cc
+CFLAGS= -g $(INCLUDES)
+F77= gfortran
+FFLAGS= -g -fdec -std=legacy -L/usr/lib -lgfortran -C
+
+FLIBS = -lutil -lm
+#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm
+XLIBS= -lXaw -lXt -lXmu -lXext -lX11  
+LFLAGS= $(FLIBS)
+XLFLAGS= $(FLIBS) $(XLIBS) 
+
+LD = gfortran
+CLD = gfortran
+#CLD = cc
+LDFLAGS = -g # Comment out for faster linking when debugging
+
+
+
+#
+# Sequence library handling routines
+#
+SEQLIB=\
+	seqlibsubs.o
+
+
+#
+# The C objects, needed by every X program
+#
+CCORE=\
+	postscript.o\
+	Graph.o\
+	plotLog.o\
+	help.o\
+	dialogues.o\
+	userfacecom.o\
+	helpnmenu.o\
+	xmenu.o\
+	FtoC.o\
+	mcspec.o\
+	locks.o
+
+COBJS=\
+	main.o\
+	$(CCORE)
+
+XDAPCOBJS=\
+	xdapmain.o\
+	$(CCORE)
+
+
+#
+# Common objects, needed by every program
+#
+COMMONOBJSB=\
+	fmain.o\
+	seeme-aix.o\
+	nxspec.o\
+	userface.o\
+	userfacecom.o\
+	nxhelpmenu.o\
+	helpnmenu.o\
+	FtoC.o\
+	subs89.a
+
+COMMONOBJS=\
+	$(COMMONOBJSB)\
+	postscript.o
+
+SCOMMONOBJS=\
+	$(COMMONOBJSB)
+
+XCOMMONOBJS=\
+	seeme-aix.o\
+	xspec.o\
+	subs89.a\
+	$(COBJS)
+
+XDAPCOMMONOBJS=\
+	seeme-aix.o\
+	xspec.o\
+	subs89.a\
+	$(XDAPCOBJS)
+
+
+#
+# Building the programs
+# This should be just a linking phase because all of the object
+# files and library files are generated using implicit rules.
+# We use the fortran compiler to do linking.
+#
+GIP=\
+	gip.o
+
+GIPOBJS=\
+	$(GIP)\
+	$(SCOMMONOBJS)
+
+gip: $(GIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(GIPOBJS) $(LFLAGS)
+
+
+LIP=\
+	lip.o
+ 
+LIPOBJS=\
+	$(LIP)\
+	$(SEQLIB)\
+	$(COMMONOBJS)
+ 
+lip: $(LIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(LIPOBJS) $(LFLAGS)
+
+
+MEP=\
+	mep.o\
+	mepsub.o\
+	asubs89.a\
+	plot92.a
+
+MEPOBJS=\
+	$(MEP)\
+	$(COMMONOBJS)\
+	pl4010.o
+
+XMEPOBJS=\
+	$(MEP)\
+	$(XCOMMONOBJS)\
+	plX.o\
+	textOutput.o 
+
+mep: $(MEPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(MEPOBJS)  $(LFLAGS)
+
+xmep: $(XMEPOBJS)
+	$(CLD) $(LDFLAGS) -o $@ $(XMEPOBJS) $(XLFLAGS)
+
+
+
+
+NIP=\
+	nip.o\
+	patternn.a\
+	patternnc.a\
+	anals89.a\
+	asubs89.a\
+	plot92.a \
+	$(SEQLIB)
+
+NIPOBJS=\
+	$(NIP)\
+	$(COMMONOBJS)\
+	pl4010.o
+
+XNIPOBJS=\
+	$(NIP)\
+	$(XCOMMONOBJS)\
+	plX.o\
+	textOutput.o 
+
+nip: $(NIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)
+
+xnip: $(XNIPOBJS)
+	$(CLD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)
+
+
+
+
+NIPL=\
+	nipl.o\
+	patternnc.a\
+	anals89.a\
+	asubs89.a\
+	$(SEQLIB)
+
+NIPLOBJS=\
+	$(NIPL)\
+	$(SCOMMONOBJS)
+
+nipl: $(NIPLOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(NIPLOBJS) $(LFLAGS)
+
+
+
+NIPF=\
+	nipf.o\
+	asubs89.a\
+	plot92.a
+
+NIPFOBJS=\
+	$(NIPF)\
+	$(COMMONOBJS)\
+	pl4010.o
+
+
+nipf: $(NIPFOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(NIPFOBJS) $(LFLAGS)
+
+
+
+
+
+PIP=\
+	pip.o\
+	analps89.a\
+	patternp.a\
+	patternpc.a\
+	asubs89.a\
+	plot92.a\
+	$(SEQLIB)
+
+PIPOBJS=\
+	$(PIP)\
+	$(COMMONOBJS)\
+	pl4010.o
+
+XPIPOBJS=\
+	$(PIP)\
+	$(XCOMMONOBJS)\
+	plX.o\
+	textOutput.o 
+
+pip: $(PIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(PIPOBJS)  $(LFLAGS)
+
+xpip:$(XPIPOBJS)
+	$(CLD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)
+
+
+
+
+PIPL=\
+	pipl.o\
+	patternpc.a\
+	analps89.a\
+	asubs89.a\
+	$(SEQLIB)
+
+PIPLOBJS=\
+	$(PIPL)\
+	$(SCOMMONOBJS)
+
+pipl: $(PIPLOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(PIPLOBJS)  $(LFLAGS)
+
+
+
+#
+# Trace manager objects
+#
+STDTEDFILES=\
+	seq.o\
+	seqIOABI.o\
+	seqIOALF.o\
+	seqIOSCF.o\
+	seqIOPlain.o\
+	opp.o\
+	fpoint.o\
+	mach-io.o
+
+TMANOBJS=\
+	tman_main.o\
+	tman_display.o\
+	tman_traceDisplay.o\
+	tman_basesDisplay.o\
+	tman_context.o\
+	tman_gadgets.o\
+	$(STDTEDFILES)
+
+# Some versions of X11R4 may have a bug in SmeLine.c
+XHACK=\
+	SmeLine.o
+
+EDITOR=\
+	$(XHACK)\
+	xsapConEdit.o\
+	contigEditor.o\
+	edUtils.o\
+	undo.o\
+	Sheet.o\
+	select.o\
+	extend.o\
+	searchUtils.o\
+	edMenu.o\
+	trans.o\
+	$(MISCBIN)/misc.a
+
+TAGEDITOR=\
+	tagEditor.o\
+	tagdbparse.o\
+	tagU2.o\
+	tagU1.o
+
+DAP=\
+	dap.o\
+	dbsysnew.o\
+	dbsyscommon.o\
+	asubs89.a\
+	plot92.a
+
+DAPOBJS=\
+	$(DAP)\
+	$(COMMONOBJS)\
+	pl4010.o\
+	conEdit.o\
+	tagU2.o
+
+XDAPOBJS=\
+	$(DAP)\
+	$(XDAPCOMMONOBJS)\
+	plX.o\
+	textOutput.o\
+	$(EDITOR)\
+	$(TMANOBJS)\
+	$(TAGEDITOR)
+
+dap: $(DAPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(DAPOBJS) $(LFLAGS)
+
+xdap: $(XDAPOBJS)
+	$(CLD) $(LDFLAGS) -o $@ $(XDAPOBJS) $(XLFLAGS)
+
+convert_project: cvt.o
+	$(CC) $(CFLAGS) -o $@ cvt.o
+
+SAP=\
+	sap.o\
+	dbsyscommon.o\
+	dbsysold.o\
+	asubs89.a\
+	plot92.a
+
+SAPOBJS=\
+	$(SAP)\
+	$(COMMONOBJS)\
+	pl4010.o
+
+XSAPOBJS=\
+	$(SAP)\
+	$(XCOMMONOBJS)\
+	plX.o\
+	textOutput.o 
+
+sap: $(SAPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)
+
+xsap: $(XSAPOBJS)
+	$(CLD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)
+
+
+
+
+SAPF=\
+	sapf.o\
+	dbsyscommon.o\
+	dbsysold.o\
+	asubs89.a\
+	plot92.a
+
+SAPFOBJS=\
+	$(SAPF)\
+	sapmen.o\
+	$(COMMONOBJS)\
+	pl4010.o
+
+sapf: $(SAPFOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)
+
+
+
+
+
+
+SIP=\
+	sip.o\
+	dias89.a\
+	plot92.a\
+	$(SEQLIB)
+
+SIPOBJS=\
+	$(SIP)\
+	$(COMMONOBJS)\
+	pl4010.o
+
+XSIPOBJS=\
+	$(SIP)\
+	$(XCOMMONOBJS)\
+	plX.o\
+	textOutput.o 
+
+sip: $(SIPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)
+
+xsip: $(XSIPOBJS)
+	$(CLD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)
+
+
+
+
+SIPL=\
+	sipl.o\
+	dias89.a\
+	$(SEQLIB)
+
+SIPLOBJS=\
+	$(SIPL)\
+	$(SCOMMONOBJS)
+
+sipl: $(SIPLOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)
+
+
+
+
+SETHELP=\
+	sethelp.o
+
+SETHELPOBJS=\
+	$(SETHELP)
+
+sethelp: $(SETHELPOBJS)
+	$(CLD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)
+
+
+
+
+SPLITP1=\
+	splitp1.o
+SPLITP1OBJS=\
+	$(SPLITP1)\
+	$(SCOMMONOBJS)
+
+splitp1: $(SPLITP1OBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)
+
+
+
+
+SPLITP2=\
+	splitp2.o
+SPLITP2OBJS=\
+	$(SPLITP2)\
+	$(SCOMMONOBJS)
+
+splitp2: $(SPLITP2OBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)
+
+
+
+
+
+SPLITP3=\
+	splitp3.o
+SPLITP3OBJS=\
+	$(SPLITP3)\
+	$(SCOMMONOBJS)
+
+splitp3: $(SPLITP3OBJS)
+	$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)
+
+
+
+REP=\
+	rep.o\
+	dias89.a\
+	subs89.a
+
+REPOBJS=\
+	$(REP)\
+	$(COMMONOBJS)
+ 
+rep:	$(REPOBJS)
+	$(F77) $(LDFLAGS) -o $@ $(REPOBJS) $(LFLAGS)
+
+
+
+
+
+VEP=\
+	vep.o\
+	dias89.a\
+	subs89.a
+
+
+VEPOBJS=\
+	$(VEP)\
+	$(SCOMMONOBJS)
+
+
+vep: $(VEPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(VEPOBJS)  $(LFLAGS)
+
+
+
+
+#
+# Special dependencies
+#
+#
+
+#
+# Files requiring simple C compilation (thing.c -> thing.o)
+# 
+%.o: $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+%.o: $(TEDSRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
+# 
+%.o: $(SRC)/%.f
+	$(F77) $(FFLAGS) -c $<
+
+
+#
+# The UNIX library (archive) mechanism is fairly weak so the following
+# procedure is used to generate libraries.
+#   * split the source file up into files which each contain
+#     a single function or subroutine
+#   * compile each of those files
+#   * insert the object files individually into the library
+# Each library is built by using a temporary directory.
+# The fortran compilations must be done sequentially in order to
+# avoid filling up the (small on this machine) /tmp directory
+# with compiler debugging information.
+#
+%.a: $(SRC)/%.f
+	sh gen_a.sh
+
+#	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 $@; \
+#	ar rcv $@ *.o; \
+#	ranlib $@; \
+##rm *.o; \
+#
+#	cd $$BINDIR; \
+#	rm -r $$TMPDIR
+
+
+
+#.f.a:
+#	$(F77) $(FFLAGS) -c $<
+#	ar rcv $@ $*.o
+#	ranlib $@
+#	rm $*.o
+
+all: $(PROGS)
+
+nprogs: $(NPROGS)
+
+xprogs: $(XPROGS)
+
+lprogs: $(LPROGS)
+
+clean:
+	rm -f $(PROGS) *.a *.o *~
+
+lint:
+	lint -Q -Nn5000 -DNOSTRDUP $(INCLUDES) *.c
+
+
diff --git a/src/staden/makefile-alpha b/src/staden/makefile-alpha
index 2b98054..f9b9043 100644
--- a/src/staden/makefile-alpha
+++ b/src/staden/makefile-alpha
@@ -19,27 +19,25 @@ PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
 SRC=.
 TEDSRC=$(SRC)/../ted
 MISCSRC=$(SRC)/../Misc
-MISCBIN=$(MISCSRC)
+MISCBIN=$(MISCSRC)/alpha-binaries
 INCLUDES= -I$(SRC) -I$(TEDSRC) -I$(MISCSRC)
 
 #
 # Compilers and flags
 #
 CC= cc
-CFLAGS= -g $(INCLUDES)
-F77= gfortran
-FFLAGS= -g -fdec -std=legacy -L/usr/lib -lgfortran -C
+CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES)
+F77= f77
+FFLAGS= -g -C
 
-FLIBS = -lutil -lm
-#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm
-XLIBS= -lXaw -lXt -lXmu -lXext -lX11  
+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 = gfortran
-CLD = gfortran
-#CLD = cc
-LDFLAGS = -g # Comment out for faster linking when debugging
+LD = f77
+CLD = cc
+LDFLAGS = -g -non_shared # Comment out for faster linking when debugging
 
 
 
@@ -80,7 +78,7 @@ XDAPCOBJS=\
 #
 COMMONOBJSB=\
 	fmain.o\
-	seeme-aix.o\
+	seeme-dec.o\
 	nxspec.o\
 	userface.o\
 	userfacecom.o\
@@ -97,13 +95,13 @@ SCOMMONOBJS=\
 	$(COMMONOBJSB)
 
 XCOMMONOBJS=\
-	seeme-aix.o\
+	seeme-dec.o\
 	xspec.o\
 	subs89.a\
 	$(COBJS)
 
 XDAPCOMMONOBJS=\
-	seeme-aix.o\
+	seeme-dec.o\
 	xspec.o\
 	subs89.a\
 	$(XDAPCOBJS)
@@ -551,34 +549,25 @@ vep: $(VEPOBJS)
 # avoid filling up the (small on this machine) /tmp directory
 # with compiler debugging information.
 #
-%.a: $(SRC)/%.f
-	sh gen_a.sh
-
-#	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 $@; \
-#	ar rcv $@ *.o; \
-#	ranlib $@; \
-##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
 
 #.f.a:
 #	$(F77) $(FFLAGS) -c $<
diff --git a/src/ted/makefile b/src/ted/makefile
new file mode 100644
index 0000000..dbcc3c2
--- /dev/null
+++ b/src/ted/makefile
@@ -0,0 +1,90 @@
+#
+# Makefile for ted (trace editor) - Alpha fork
+#
+
+#
+#Turning on the AUTO_CLIP switch allows ted to automatically
+#select a left (using the -enzyme option or the .enzyme in the
+#Xted file) and right cutoff on your sequence (using 2 out of
+#5 N's)
+#
+# Turning on the SAVE_EDITS switch allows the user to maintain
+# copies of their edits, i.e. when you open up ted on a file
+# that you have already edited, the old edits show up in the
+# ted edit window.  The user may also call up any of their
+# past editing sessions.  
+#
+#Turning on the DEF_OUT  switch makes
+# trace_name.seq the default output file name
+#
+#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS
+SWITCHES = -DAUTO_CLIP
+
+#
+# Programs made by this makefile
+#
+PROGS = ted
+
+#
+# Where the wild things are
+#
+SRC = .
+
+#
+# Compiler - debug on
+#
+CC= gfortran
+INCLUDES = -I$(SRC)
+CFLAGS= -g $(SWITCHES) $(INCLUDES)
+LIBS= -lXaw -lXt -lXmu -lXext -lX11 
+#-ldnet_stub
+#
+LD= gfortran
+LDFLAGS= -g 
+
+#
+# Object files
+#
+TEDOBJS=\
+	ted.o\
+	dialogues.o\
+	seq.o\
+	seqIOPlain.o\
+	seqIOABI.o\
+	help.o\
+	display.o\
+	traceDisplay.o\
+	basesDisplay.o\
+	Graph.o\
+	seqIOEdit.o\
+	seqIOALF.o\
+	seqIOSCF.o\
+	seqOutput.o\
+	opp.o\
+	info.o\
+	fpoint.o\
+	mach-io.o\
+	seqRead.o
+
+
+#
+# Linking
+#
+ted: $(TEDOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(TEDOBJS) $(LIBS)
+
+#
+# Files requiring simple C compilation (thing.c -> thing.o)
+# 
+%.o : $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+
+#
+# Special dependencies
+#
+clean:
+	rm -f ted $(TEDOBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
+
+all: $(PROGS)
+
diff --git a/src/ted/makefile-alpha b/src/ted/makefile-alpha
index dbcc3c2..e571a12 100644
--- a/src/ted/makefile-alpha
+++ b/src/ted/makefile-alpha
@@ -33,14 +33,13 @@ SRC = .
 #
 # Compiler - debug on
 #
-CC= gfortran
+CC= cc
 INCLUDES = -I$(SRC)
-CFLAGS= -g $(SWITCHES) $(INCLUDES)
-LIBS= -lXaw -lXt -lXmu -lXext -lX11 
-#-ldnet_stub
+CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES)
+LIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub
 #
-LD= gfortran
-LDFLAGS= -g 
+LD= cc
+LDFLAGS= -g -non_shared
 
 #
 # Object files
diff --git a/src/update_subclones/makefile b/src/update_subclones/makefile
new file mode 100644
index 0000000..a24c246
--- /dev/null
+++ b/src/update_subclones/makefile
@@ -0,0 +1,42 @@
+#
+# Makefile for subclonedb
+#
+
+#
+# Programs made by this makefile
+#
+PROGS = update_subclones
+
+#
+# Where the wild things are
+#
+SRC = .
+MISCSRC = $(SRC)/../Misc
+MISCBIN = $(MISCSRC)
+INCLUDES = -I$(SRC) -I$(MISCSRC)
+
+#
+# Alpha
+#
+CC = cc
+CFLAGS = -g $(INCLUDES)
+LD = cc
+LDFLAGS = -g 
+
+#
+# Here they are
+#
+
+update_subclones : update_subclones.o $(MISCBIN)/misc.a
+	$(LD) $(LDFLAGS) -o update_subclones update_subclones.o $(MISCBIN)/misc.a
+
+#
+# Special dependencies
+#
+all: $(PROGS)
+
+clean:
+	/bin/rm -f $(PROGS)
+
+%.o: $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
diff --git a/src/update_subclones/makefile-alpha b/src/update_subclones/makefile-alpha
index a24c246..7f1782d 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)
+MISCBIN = $(MISCSRC)/alpha-binaries
 INCLUDES = -I$(SRC) -I$(MISCSRC)
 
 #
 # Alpha
 #
 CC = cc
-CFLAGS = -g $(INCLUDES)
+CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES)
 LD = cc
-LDFLAGS = -g 
+LDFLAGS = -g -non_shared
 
 #
 # Here they are
diff --git a/src/vepe/makefile b/src/vepe/makefile
new file mode 100644
index 0000000..68bc535
--- /dev/null
+++ b/src/vepe/makefile
@@ -0,0 +1,137 @@
+# Makefile for vepe - Alpha version
+# -------------------------------
+
+PROGS= vepe
+
+all: $(PROGS)
+
+
+
+
+
+#
+# ``Interesting'' suffices that make needs to know about
+#
+.SUFFIXES: .a $(SUFFIXES)
+
+
+#
+# Directories
+#
+SRC = .
+#STADENSRC=/nfs/rutland/home3/pubseq/inhouse/share/src/staden
+STADENSRC=$(SRC)/../staden
+STADENBIN=$(STADENSRC)
+# Use the ted sources compiled for staden executables
+INCLUDES= -I$(STADENSRC)
+
+
+#
+# Compilers and flags
+#
+# debug on
+CC= cc
+CFLAGS= -g $(INCLUDES)
+F77= gfortran
+FFLAGS= -g
+LD= gfortran
+LDFLAGS= -g 
+
+FLAGS = -lutil -lm
+#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
+XLIBS= -lXaw -lXt -lXmu -lXext -lX11
+#LFLAGS= $(FLIBS)
+XLFLAGS= $(FLIBS) $(XLIBS)
+
+#
+# Avoid compilation of objects in remote directories
+#
+$(STADENBIN)/%.o : $(STADENSRC)/%.f
+$(STADENBIN)/%.o : $(STADENSRC)/%.c
+
+#
+# Common objects, needed by every program
+#
+COMMONOBJS=\
+	$(STADENBIN)/seeme-aix.o\
+	$(STADENBIN)/nxspec.o\
+	$(STADENBIN)/userface.o\
+	$(STADENBIN)/userfacecom.o\
+	$(STADENBIN)/helpnmenu.o\
+	$(STADENBIN)/nxhelpmenu.o\
+	$(STADENBIN)/FtoC.o\
+	$(STADENBIN)/subs89.a\
+
+
+#
+# Building the programs
+# This should be just a linking phase because all of the object
+# files and library files are generated using implicit rules.
+# We use the fortran compiler to do linking.
+#
+
+#
+# Vector excision program
+#
+
+VEP=\
+	vep.o\
+	$(STADENBIN)/dias89.a\
+	$(STADENBIN)/subs89.a
+
+
+VEPOBJS=\
+	$(VEP)\
+	$(COMMONOBJS)
+
+
+vep: $(VEPOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(VEPOBJS)  $(LFLAGS)
+
+
+
+VEPE=\
+	vepe.o\
+	$(STADENBIN)/dias89.a\
+	expio.o\
+	expFileIO.o
+
+
+VEPEOBJS=\
+	$(VEPE)\
+	$(COMMONOBJS)
+
+
+vepe: $(VEPEOBJS)
+	$(LD) $(LDFLAGS) -o $@ $(VEPEOBJS)  $(LFLAGS)
+
+COBJS =  expFileIO.o testc.o
+FOBJS =  expFileIO.o testf.o
+
+
+testc: $(COBJS)
+	$(CC) $(CFLAGS) -o $@ $(COBJS)
+
+testf:  $(FOBJS)
+	$(F77) $(FFLAGS) -o $@ $(FOBJS)
+
+
+#
+# Files requiring simple C compilation (thing.c -> thing.o)
+# 
+%.o: %.c
+	$(CC) $(CFLAGS) -c $<
+%.o: $(SRC)/%.c
+	$(CC) $(CFLAGS) -c $<
+
+#
+# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
+# 
+%.o: $(SRC)/%.f
+	$(F77) $(FFLAGS) -c $<
+
+clean:
+	rm -f $(PROGS) *.o *.a *~
+
+
+install: clean all
diff --git a/src/vepe/makefile-alpha b/src/vepe/makefile-alpha
index 68bc535..ff9fb35 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=$(STADENSRC)
+STADENBIN=$(STADENSRC)/alpha-binaries
 # Use the ted sources compiled for staden executables
 INCLUDES= -I$(STADENSRC)
 
@@ -31,14 +31,13 @@ INCLUDES= -I$(STADENSRC)
 #
 # debug on
 CC= cc
-CFLAGS= -g $(INCLUDES)
-F77= gfortran
+CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES)
+F77= f77
 FFLAGS= -g
-LD= gfortran
-LDFLAGS= -g 
+LD= f77
+LDFLAGS= -g -non_shared
 
-FLAGS = -lutil -lm
-#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
+FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
 XLIBS= -lXaw -lXt -lXmu -lXext -lX11
 #LFLAGS= $(FLIBS)
 XLFLAGS= $(FLIBS) $(XLIBS)
@@ -53,7 +52,7 @@ $(STADENBIN)/%.o : $(STADENSRC)/%.c
 # Common objects, needed by every program
 #
 COMMONOBJS=\
-	$(STADENBIN)/seeme-aix.o\
+	$(STADENBIN)/seeme-dec.o\
 	$(STADENBIN)/nxspec.o\
 	$(STADENBIN)/userface.o\
 	$(STADENBIN)/userfacecom.o\