diff --git a/Staden_install-alpha b/Staden_install-alpha
deleted file mode 100644
index 34a9b69..0000000
--- a/Staden_install-alpha
+++ /dev/null
@@ -1,453 +0,0 @@
-#! /bin/csh -f
-#
-# staden_install - version 2.4
-#
-#	This is a prototype installation program.
-#
-# 9 March 1992
-#	Modified for installation on Sun, Alliant, etc
-#	No longer install 2rs
-#
-# 20 November 1992
-#	Now includes convert, cop, frog, getMCH and scf
-#
-# 25 November 1992
-#	SGI supported
-# 
-# 19 May 1993
-#	DEC Alpha, Solaris supported
-# 
-# Written by sd@uk.ac.cam.mrc-lmb
-#
-
-# prelim
-set prog = $0 ; set prog = $prog:t
-
-# Machines supported: al sun dec sgi alpha solaris
-#set MACHINE = `echo $prog | sed 's/.*-//'`
-set MACHINE = alpha
-
-# For local (MRC-LMB) setup only
-#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
-set LOCAL = NO
-
-
-echo ""
-echo -n "Staden Package installation procedure - "
-switch (${MACHINE})
-	case "al":
-		echo "Alliant FX/2800 Concentrix version"
-		set MAKE = "make -sk"
-		breaksw
-	case "sun":
-		echo "SunOS version"
-		set MAKE = "make -sk"
-		breaksw
-	case "dec":
-		echo "DEC Ultrix (mips) version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "sgi":
-		echo "Silicon Graphics Iris version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "alpha":
-		echo "DEC Alpha OSF/1 version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "solaris":
-		echo "Solaris version"
-		set MAKE = "make -sk"
-		breaksw
-	default:
-		echo "Panic. Unknown version"
-		exit 1
-endsw
-echo ""
-echo "* starting initialization...please wait."
-echo ""
-
-# Binary fork of source directory
-if ($LOCAL == "YES") then
-    set DIR_BINARIES = ${MACHINE}-binaries
-    set DIR_PROGS = ${MACHINE}-bin
-else
-    set DIR_BINARIES = .
-    set DIR_PROGS = bin
-    set MAKE = "$MAKE -f makefile-${MACHINE}"
-endif
-
-init:
-# Set useful shell variables
-set YES="YES";
-set NO="NO"
-
-# set/unset some .cshrc envs.
-unset noclobber
-set noglob
-
-# set interrupt trap
-onintr end_failure
-
-# Make dir command
-set MKDIR = "mkdir"
-
-# Copy command
-set CP = "cp -p"
-
-# Install command
-#set INSTALL = "install"
-#set INSTALL = "mv"
-set INSTALL = "cp"
-
-# Set up default responses
-set DEF_STADEN_ROOT = `pwd`
-
-set DEF_REQ_NONX = "$YES"
-set DEF_REQ_X = "$YES"
-set DEF_REQ_TED = "$YES"
-set DEF_REQ_MISC = "$YES"
-
-# directories
-set DIR_SRC = $DEF_STADEN_ROOT/src
-set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
-set DIR_MISC = $DIR_SRC/Misc
-set DIR_STADEN = $DIR_SRC/staden
-set DIR_TED = $DIR_SRC/ted
-set DIR_ABI = $DIR_SRC/abi
-set DIR_ALF = $DIR_SRC/alf
-set DIR_BAP = $DIR_SRC/bap
-set DIR_OSP = $DIR_SRC/bap/osp-bits
-set DIR_CONVERT = $DIR_SRC/convert
-set DIR_COP = $DIR_SRC/cop
-set DIR_FROG = $DIR_SRC/frog
-set DIR_GETMCH = $DIR_SRC/getMCH
-set DIR_SCF = $DIR_SRC/scf
-
-
-main:
-
-	
-preamble:
-	echo ""
-	echo ""
-	echo "* Please answer the following questions."
-	echo "  Default answers to questions are given in square brackets."
-	echo "  If you require help at any stage respond with a ? to the question."
-	echo ""
-
-ask_staden_root:
-	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
-
-ask_require_nonx_progs: 
-	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
-	set ANS_REQ_NONX = $<
-	if ("$ANS_REQ_NONX" == "?") then
-		echo "* If you do not have X windows on your system you will require"
-		echo "  these.  However, you will require Tektronics terminal emulation."
-		echo "  If you do not require all of the non-X programs, you should abort"
-		echo "  and manually make the ones you require."
-		echo ""
-		goto ask_require_nonx_progs
-	else if ("$ANS_REQ_NONX" != "") then
-		if ("$ANS_REQ_NONX" =~ [yY]*) then
-			set ANS_REQ_NONX=$YES
-		else if ("$ANS_REQ_NONX" =~ [nN]*) then
-			set ANS_REQ_NONX=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_NONX=$DEF_REQ_NONX
-	endif
-
-ask_require_x_progs:
-	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
-	set ANS_REQ_X = $<
-	if ("$ANS_REQ_X" == "?") then
-		echo "* These are the programs that require X windows."
-		echo "  If you do not require all of the X programs, you should abort"
-		echo "  and manually make the ones you require."
-
-		echo ""
-		goto ask_require_x_progs
-	else if ("$ANS_REQ_X" != "") then
-		if ("$ANS_REQ_X" =~ [yY]*) then
-			set ANS_REQ_X=$YES
-		else if ("$ANS_REQ_X" =~ [nN]*) then
-			set ANS_REQ_X=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_X=$DEF_REQ_X
-	endif
-
-
-ask_require_ted:
-	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
-	set ANS_REQ_TED = $<
-	if ("$ANS_REQ_TED" == "?") then
-		echo "* This is the trace editor program.  It allows you to look at"
-		echo "  traces obtained from automated fluorescent sequencing machines."
-		echo ""
-		goto ask_require_ted
-	else if ("$ANS_REQ_TED" != "") then
-		if ("$ANS_REQ_TED" =~ [yY]*) then
-			set ANS_REQ_TED=$YES
-		else if ("$ANS_REQ_TED" =~ [nN]*) then
-			set ANS_REQ_TED=$NO
-		else
-			goto ask_require_ted
-		endif
-	else
-		set ANS_REQ_TED=$DEF_REQ_TED
-	endif
-
-
-
-ask_require_misc:
-	echo -n "Compile other programs [$DEF_REQ_MISC]? "
-	set ANS_REQ_MISC = $<
-	if ("$ANS_REQ_MISC" == "?") then
-		echo "* Other programs include:"
-		echo "    alfsplit"
-		echo "    getABISampleName"
-		echo ""
-		goto ask_require_misc
-	else if ("$ANS_REQ_MISC" != "") then
-		if ("$ANS_REQ_MISC" =~ [yY]*) then
-			set ANS_REQ_MISC=$YES
-		else if ("$ANS_REQ_MISC" =~ [nN]*) then
-			set ANS_REQ_MISC=$NO
-		else
-			goto ask_require_misc
-		endif
-	else
-		set ANS_REQ_MISC=$DEF_REQ_MISC
-	endif
-
-
-
-time_taken_warning:
-	echo ""
-	echo "The installation procedure is now ready to start."
-	echo ""
-	echo "**** Warning:"
-	echo "    The installation will take considerable time to complete.  If you"
-	echo "    are installing the whole Staden Package from scratch it could"
-	echo "    take as long as an hour for all exectuables to be compiled and"
-	echo "    installed."
-	echo ""
-
-ask_goahead:
-	echo -n "Proceed with the installation [YES]? " 
-	set ANSWER=$<
-	if ("$ANSWER" == "?") then
-		echo "* Final confirmation to proceed with the installation.  Answer"
-		echo "  YES to proceed; otherwise, answer NO to abort the installation."
-		echo ""
-		goto ask_goahead
-	else if ("$ANSWER" != "") then
-		if ("$ANSWER" =~ [nN]*) then
-			goto chickens_exit
-		else if ("$ANSWER" !~ [yY]*) then
-			goto ask_goahead
-		endif
-	endif
-
-installation_proper:
-
-# make binaries directory if it doesn't exist
-
-	if (! -d $DIR_BIN) then
-		$MKDIR $DIR_BIN
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
-		echo ""
-		echo "+ Compiling miscellaneous library"
-
-		pushd $DIR_MISC > /dev/null
-
-		cd $DIR_BINARIES
-	        $MAKE all
-
-		popd > /dev/null
-
-	endif
-
-        if ("$ANS_REQ_NONX" == "$YES") then
-		echo ""
-		echo "+ Installing non X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE nprogs lprogs
-                $INSTALL mep $DIR_BIN
-		$INSTALL nip $DIR_BIN
-		$INSTALL pip $DIR_BIN
-		$INSTALL sap $DIR_BIN
-		$INSTALL sapf $DIR_BIN
-		$INSTALL sip $DIR_BIN
-		$INSTALL splitp1 $DIR_BIN
-		$INSTALL splitp2 $DIR_BIN
-		$INSTALL splitp3 $DIR_BIN
-		$INSTALL sethelp $DIR_BIN
-		$INSTALL gip $DIR_BIN
-		$INSTALL nipl $DIR_BIN
-		$INSTALL pipl $DIR_BIN
-		$INSTALL sipl $DIR_BIN
-		$INSTALL dap $DIR_BIN
-		$INSTALL nipf $DIR_BIN
-		$INSTALL vep $DIR_BIN
-		$INSTALL rep $DIR_BIN
-		$INSTALL lip $DIR_BIN
-		#$INSTALL convert_project $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE bap
-                $INSTALL bap $DIR_BIN
-		popd > /dev/null
-
-	endif
-
-	if ("$ANS_REQ_TED" == "$YES") then
-		echo ""
-		echo "+ Installing Trace editor"
-
-		pushd $DIR_TED > /dev/null
-		cd $DIR_BINARIES
-                $MAKE ted
-		$INSTALL ted $DIR_BIN
-		popd > /dev/null
-	endif
-
-	if ("$ANS_REQ_X" == "$YES") then
-		echo ""
-		echo "+ Installing X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-                $MAKE xprogs
-		$INSTALL xmep $DIR_BIN
-		$INSTALL xnip $DIR_BIN
-		$INSTALL xpip $DIR_BIN
-		$INSTALL xsap $DIR_BIN
-		$INSTALL xsip $DIR_BIN
-		$INSTALL xdap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE xbap
-                $INSTALL xbap $DIR_BIN
-		popd > /dev/null
-
-
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES") then
-		echo ""
-		echo "+ Installing miscellaneous programs"
-
-		pushd $DIR_ABI > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL getABISampleName $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_ALF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE alfsplit
-		$INSTALL alfsplit $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_CONVERT > /dev/null
-		cd $DIR_BINARIES
-                $MAKE convert
-		$INSTALL convert $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_COP > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL cop $DIR_BIN
-		$INSTALL cop-bap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_FROG > /dev/null
-		cd $DIR_BINARIES
-                $MAKE frog
-		$INSTALL frog $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_GETMCH > /dev/null
-		cd $DIR_BINARIES
-                $MAKE trace2seq
-		$INSTALL trace2seq $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_SCF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE makeSCF
-		$INSTALL makeSCF $DIR_BIN
-		popd > /dev/null
-
-
-
-	endif
-
-
-installation_done:
-	echo ""
-	echo "+ Installation completed"
-	echo ""
-
-	echo "  Some further initialisation is required in order to use the"
-	echo "  package.  csh users should insert the following in their .login"
-	echo "  files:"
-	echo "  "
-	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
-	echo '  	source $STADENROOT/staden.login'
-	echo "  "
-	echo "  Users of the Bourne shell, sh, should insert the following in"
-	echo "  their .profile:"
-	echo "  "
-	echo "  	STADENROOT=$ANS_STADEN_ROOT"
-	echo "  	export STADENROOT"
-	echo '  	. $STADENROOT/staden.profile'
-	echo "  "
-	echo "  These initialisations will alter the shell's search path so that"
-	echo "  it can find the programs in the STADEN Package"
-	echo "  "
-
-normal_exit:
-	exit 0
-
-chickens_exit:
-	echo ""
-	echo "+ Installation cancelled"
-	echo ""
-
-	exit 0
-
-end_failure:
-	unset noglob
-	echo ""
-	echo "Aborted STADEN Package installation on `date`" 
-	echo ""
-	exit 1
-
diff --git a/Staden_install-dec b/Staden_install-dec
deleted file mode 100644
index 9b06240..0000000
--- a/Staden_install-dec
+++ /dev/null
@@ -1,453 +0,0 @@
-#! /bin/csh -f
-#
-# staden_install - version 2.4
-#
-#	This is a prototype installation program.
-#
-# 9 March 1992
-#	Modified for installation on Sun, Alliant, etc
-#	No longer install 2rs
-#
-# 20 November 1992
-#	Now includes convert, cop, frog, getMCH and scf
-#
-# 25 November 1992
-#	SGI supported
-# 
-# 19 May 1993
-#	DEC Alpha, Solaris supported
-# 
-# Written by sd@uk.ac.cam.mrc-lmb
-#
-
-# prelim
-set prog = $0 ; set prog = $prog:t
-
-# Machines supported: al sun dec sgi alpha solaris
-#set MACHINE = `echo $prog | sed 's/.*-//'`
-set MACHINE = dec
-
-# For local (MRC-LMB) setup only
-#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
-set LOCAL = NO
-
-
-echo ""
-echo -n "Staden Package installation procedure - "
-switch (${MACHINE})
-	case "al":
-		echo "Alliant FX/2800 Concentrix version"
-		set MAKE = "make -sk"
-		breaksw
-	case "sun":
-		echo "SunOS version"
-		set MAKE = "make -sk"
-		breaksw
-	case "dec":
-		echo "DEC Ultrix (mips) version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "sgi":
-		echo "Silicon Graphics Iris version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "alpha":
-		echo "DEC Alpha OSF/1 version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "solaris":
-		echo "Solaris version"
-		set MAKE = "make -sk"
-		breaksw
-	default:
-		echo "Panic. Unknown version"
-		exit 1
-endsw
-echo ""
-echo "* starting initialization...please wait."
-echo ""
-
-# Binary fork of source directory
-if ($LOCAL == "YES") then
-    set DIR_BINARIES = ${MACHINE}-binaries
-    set DIR_PROGS = ${MACHINE}-bin
-else
-    set DIR_BINARIES = .
-    set DIR_PROGS = bin
-    set MAKE = "$MAKE -f makefile-${MACHINE}"
-endif
-
-init:
-# Set useful shell variables
-set YES="YES";
-set NO="NO"
-
-# set/unset some .cshrc envs.
-unset noclobber
-set noglob
-
-# set interrupt trap
-onintr end_failure
-
-# Make dir command
-set MKDIR = "mkdir"
-
-# Copy command
-set CP = "cp -p"
-
-# Install command
-#set INSTALL = "install"
-#set INSTALL = "mv"
-set INSTALL = "cp"
-
-# Set up default responses
-set DEF_STADEN_ROOT = `pwd`
-
-set DEF_REQ_NONX = "$YES"
-set DEF_REQ_X = "$YES"
-set DEF_REQ_TED = "$YES"
-set DEF_REQ_MISC = "$YES"
-
-# directories
-set DIR_SRC = $DEF_STADEN_ROOT/src
-set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
-set DIR_MISC = $DIR_SRC/Misc
-set DIR_STADEN = $DIR_SRC/staden
-set DIR_TED = $DIR_SRC/ted
-set DIR_ABI = $DIR_SRC/abi
-set DIR_ALF = $DIR_SRC/alf
-set DIR_BAP = $DIR_SRC/bap
-set DIR_OSP = $DIR_SRC/bap/osp-bits
-set DIR_CONVERT = $DIR_SRC/convert
-set DIR_COP = $DIR_SRC/cop
-set DIR_FROG = $DIR_SRC/frog
-set DIR_GETMCH = $DIR_SRC/getMCH
-set DIR_SCF = $DIR_SRC/scf
-
-
-main:
-
-	
-preamble:
-	echo ""
-	echo ""
-	echo "* Please answer the following questions."
-	echo "  Default answers to questions are given in square brackets."
-	echo "  If you require help at any stage respond with a ? to the question."
-	echo ""
-
-ask_staden_root:
-	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
-
-ask_require_nonx_progs: 
-	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
-	set ANS_REQ_NONX = $<
-	if ("$ANS_REQ_NONX" == "?") then
-		echo "* If you do not have X windows on your system you will require"
-		echo "  these.  However, you will require Tektronics terminal emulation."
-		echo "  If you do not require all of the non-X programs, you should abort"
-		echo "  and manually make the ones you require."
-		echo ""
-		goto ask_require_nonx_progs
-	else if ("$ANS_REQ_NONX" != "") then
-		if ("$ANS_REQ_NONX" =~ [yY]*) then
-			set ANS_REQ_NONX=$YES
-		else if ("$ANS_REQ_NONX" =~ [nN]*) then
-			set ANS_REQ_NONX=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_NONX=$DEF_REQ_NONX
-	endif
-
-ask_require_x_progs:
-	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
-	set ANS_REQ_X = $<
-	if ("$ANS_REQ_X" == "?") then
-		echo "* These are the programs that require X windows."
-		echo "  If you do not require all of the X programs, you should abort"
-		echo "  and manually make the ones you require."
-
-		echo ""
-		goto ask_require_x_progs
-	else if ("$ANS_REQ_X" != "") then
-		if ("$ANS_REQ_X" =~ [yY]*) then
-			set ANS_REQ_X=$YES
-		else if ("$ANS_REQ_X" =~ [nN]*) then
-			set ANS_REQ_X=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_X=$DEF_REQ_X
-	endif
-
-
-ask_require_ted:
-	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
-	set ANS_REQ_TED = $<
-	if ("$ANS_REQ_TED" == "?") then
-		echo "* This is the trace editor program.  It allows you to look at"
-		echo "  traces obtained from automated fluorescent sequencing machines."
-		echo ""
-		goto ask_require_ted
-	else if ("$ANS_REQ_TED" != "") then
-		if ("$ANS_REQ_TED" =~ [yY]*) then
-			set ANS_REQ_TED=$YES
-		else if ("$ANS_REQ_TED" =~ [nN]*) then
-			set ANS_REQ_TED=$NO
-		else
-			goto ask_require_ted
-		endif
-	else
-		set ANS_REQ_TED=$DEF_REQ_TED
-	endif
-
-
-
-ask_require_misc:
-	echo -n "Compile other programs [$DEF_REQ_MISC]? "
-	set ANS_REQ_MISC = $<
-	if ("$ANS_REQ_MISC" == "?") then
-		echo "* Other programs include:"
-		echo "    alfsplit"
-		echo "    getABISampleName"
-		echo ""
-		goto ask_require_misc
-	else if ("$ANS_REQ_MISC" != "") then
-		if ("$ANS_REQ_MISC" =~ [yY]*) then
-			set ANS_REQ_MISC=$YES
-		else if ("$ANS_REQ_MISC" =~ [nN]*) then
-			set ANS_REQ_MISC=$NO
-		else
-			goto ask_require_misc
-		endif
-	else
-		set ANS_REQ_MISC=$DEF_REQ_MISC
-	endif
-
-
-
-time_taken_warning:
-	echo ""
-	echo "The installation procedure is now ready to start."
-	echo ""
-	echo "**** Warning:"
-	echo "    The installation will take considerable time to complete.  If you"
-	echo "    are installing the whole Staden Package from scratch it could"
-	echo "    take as long as an hour for all exectuables to be compiled and"
-	echo "    installed."
-	echo ""
-
-ask_goahead:
-	echo -n "Proceed with the installation [YES]? " 
-	set ANSWER=$<
-	if ("$ANSWER" == "?") then
-		echo "* Final confirmation to proceed with the installation.  Answer"
-		echo "  YES to proceed; otherwise, answer NO to abort the installation."
-		echo ""
-		goto ask_goahead
-	else if ("$ANSWER" != "") then
-		if ("$ANSWER" =~ [nN]*) then
-			goto chickens_exit
-		else if ("$ANSWER" !~ [yY]*) then
-			goto ask_goahead
-		endif
-	endif
-
-installation_proper:
-
-# make binaries directory if it doesn't exist
-
-	if (! -d $DIR_BIN) then
-		$MKDIR $DIR_BIN
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
-		echo ""
-		echo "+ Compiling miscellaneous library"
-
-		pushd $DIR_MISC > /dev/null
-
-		cd $DIR_BINARIES
-	        $MAKE all
-
-		popd > /dev/null
-
-	endif
-
-        if ("$ANS_REQ_NONX" == "$YES") then
-		echo ""
-		echo "+ Installing non X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE nprogs lprogs
-                $INSTALL mep $DIR_BIN
-		$INSTALL nip $DIR_BIN
-		$INSTALL pip $DIR_BIN
-		$INSTALL sap $DIR_BIN
-		$INSTALL sapf $DIR_BIN
-		$INSTALL sip $DIR_BIN
-		$INSTALL splitp1 $DIR_BIN
-		$INSTALL splitp2 $DIR_BIN
-		$INSTALL splitp3 $DIR_BIN
-		$INSTALL sethelp $DIR_BIN
-		$INSTALL gip $DIR_BIN
-		$INSTALL nipl $DIR_BIN
-		$INSTALL pipl $DIR_BIN
-		$INSTALL sipl $DIR_BIN
-		$INSTALL dap $DIR_BIN
-		$INSTALL nipf $DIR_BIN
-		$INSTALL vep $DIR_BIN
-		$INSTALL rep $DIR_BIN
-		$INSTALL lip $DIR_BIN
-		#$INSTALL convert_project $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE bap
-                $INSTALL bap $DIR_BIN
-		popd > /dev/null
-
-	endif
-
-	if ("$ANS_REQ_TED" == "$YES") then
-		echo ""
-		echo "+ Installing Trace editor"
-
-		pushd $DIR_TED > /dev/null
-		cd $DIR_BINARIES
-                $MAKE ted
-		$INSTALL ted $DIR_BIN
-		popd > /dev/null
-	endif
-
-	if ("$ANS_REQ_X" == "$YES") then
-		echo ""
-		echo "+ Installing X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-                $MAKE xprogs
-		$INSTALL xmep $DIR_BIN
-		$INSTALL xnip $DIR_BIN
-		$INSTALL xpip $DIR_BIN
-		$INSTALL xsap $DIR_BIN
-		$INSTALL xsip $DIR_BIN
-		$INSTALL xdap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE xbap
-                $INSTALL xbap $DIR_BIN
-		popd > /dev/null
-
-
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES") then
-		echo ""
-		echo "+ Installing miscellaneous programs"
-
-		pushd $DIR_ABI > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL getABISampleName $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_ALF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE alfsplit
-		$INSTALL alfsplit $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_CONVERT > /dev/null
-		cd $DIR_BINARIES
-                $MAKE convert
-		$INSTALL convert $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_COP > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL cop $DIR_BIN
-		$INSTALL cop-bap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_FROG > /dev/null
-		cd $DIR_BINARIES
-                $MAKE frog
-		$INSTALL frog $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_GETMCH > /dev/null
-		cd $DIR_BINARIES
-                $MAKE trace2seq
-		$INSTALL trace2seq $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_SCF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE makeSCF
-		$INSTALL makeSCF $DIR_BIN
-		popd > /dev/null
-
-
-
-	endif
-
-
-installation_done:
-	echo ""
-	echo "+ Installation completed"
-	echo ""
-
-	echo "  Some further initialisation is required in order to use the"
-	echo "  package.  csh users should insert the following in their .login"
-	echo "  files:"
-	echo "  "
-	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
-	echo '  	source $STADENROOT/staden.login'
-	echo "  "
-	echo "  Users of the Bourne shell, sh, should insert the following in"
-	echo "  their .profile:"
-	echo "  "
-	echo "  	STADENROOT=$ANS_STADEN_ROOT"
-	echo "  	export STADENROOT"
-	echo '  	. $STADENROOT/staden.profile'
-	echo "  "
-	echo "  These initialisations will alter the shell's search path so that"
-	echo "  it can find the programs in the STADEN Package"
-	echo "  "
-
-normal_exit:
-	exit 0
-
-chickens_exit:
-	echo ""
-	echo "+ Installation cancelled"
-	echo ""
-
-	exit 0
-
-end_failure:
-	unset noglob
-	echo ""
-	echo "Aborted STADEN Package installation on `date`" 
-	echo ""
-	exit 1
-
diff --git a/Staden_install-sgi b/Staden_install-sgi
deleted file mode 100644
index 7ce5b1e..0000000
--- a/Staden_install-sgi
+++ /dev/null
@@ -1,453 +0,0 @@
-#! /bin/csh -f
-#
-# staden_install - version 2.4
-#
-#	This is a prototype installation program.
-#
-# 9 March 1992
-#	Modified for installation on Sun, Alliant, etc
-#	No longer install 2rs
-#
-# 20 November 1992
-#	Now includes convert, cop, frog, getMCH and scf
-#
-# 25 November 1992
-#	SGI supported
-# 
-# 19 May 1993
-#	DEC Alpha, Solaris supported
-# 
-# Written by sd@uk.ac.cam.mrc-lmb
-#
-
-# prelim
-set prog = $0 ; set prog = $prog:t
-
-# Machines supported: al sun dec sgi alpha solaris
-#set MACHINE = `echo $prog | sed 's/.*-//'`
-set MACHINE = sgi
-
-# For local (MRC-LMB) setup only
-#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
-set LOCAL = NO
-
-
-echo ""
-echo -n "Staden Package installation procedure - "
-switch (${MACHINE})
-	case "al":
-		echo "Alliant FX/2800 Concentrix version"
-		set MAKE = "make -sk"
-		breaksw
-	case "sun":
-		echo "SunOS version"
-		set MAKE = "make -sk"
-		breaksw
-	case "dec":
-		echo "DEC Ultrix (mips) version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "sgi":
-		echo "Silicon Graphics Iris version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "alpha":
-		echo "DEC Alpha OSF/1 version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "solaris":
-		echo "Solaris version"
-		set MAKE = "make -sk"
-		breaksw
-	default:
-		echo "Panic. Unknown version"
-		exit 1
-endsw
-echo ""
-echo "* starting initialization...please wait."
-echo ""
-
-# Binary fork of source directory
-if ($LOCAL == "YES") then
-    set DIR_BINARIES = ${MACHINE}-binaries
-    set DIR_PROGS = ${MACHINE}-bin
-else
-    set DIR_BINARIES = .
-    set DIR_PROGS = bin
-    set MAKE = "$MAKE -f makefile-${MACHINE}"
-endif
-
-init:
-# Set useful shell variables
-set YES="YES";
-set NO="NO"
-
-# set/unset some .cshrc envs.
-unset noclobber
-set noglob
-
-# set interrupt trap
-onintr end_failure
-
-# Make dir command
-set MKDIR = "mkdir"
-
-# Copy command
-set CP = "cp -p"
-
-# Install command
-#set INSTALL = "install"
-#set INSTALL = "mv"
-set INSTALL = "cp"
-
-# Set up default responses
-set DEF_STADEN_ROOT = `pwd`
-
-set DEF_REQ_NONX = "$YES"
-set DEF_REQ_X = "$YES"
-set DEF_REQ_TED = "$YES"
-set DEF_REQ_MISC = "$YES"
-
-# directories
-set DIR_SRC = $DEF_STADEN_ROOT/src
-set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
-set DIR_MISC = $DIR_SRC/Misc
-set DIR_STADEN = $DIR_SRC/staden
-set DIR_TED = $DIR_SRC/ted
-set DIR_ABI = $DIR_SRC/abi
-set DIR_ALF = $DIR_SRC/alf
-set DIR_BAP = $DIR_SRC/bap
-set DIR_OSP = $DIR_SRC/bap/osp-bits
-set DIR_CONVERT = $DIR_SRC/convert
-set DIR_COP = $DIR_SRC/cop
-set DIR_FROG = $DIR_SRC/frog
-set DIR_GETMCH = $DIR_SRC/getMCH
-set DIR_SCF = $DIR_SRC/scf
-
-
-main:
-
-	
-preamble:
-	echo ""
-	echo ""
-	echo "* Please answer the following questions."
-	echo "  Default answers to questions are given in square brackets."
-	echo "  If you require help at any stage respond with a ? to the question."
-	echo ""
-
-ask_staden_root:
-	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
-
-ask_require_nonx_progs: 
-	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
-	set ANS_REQ_NONX = $<
-	if ("$ANS_REQ_NONX" == "?") then
-		echo "* If you do not have X windows on your system you will require"
-		echo "  these.  However, you will require Tektronics terminal emulation."
-		echo "  If you do not require all of the non-X programs, you should abort"
-		echo "  and manually make the ones you require."
-		echo ""
-		goto ask_require_nonx_progs
-	else if ("$ANS_REQ_NONX" != "") then
-		if ("$ANS_REQ_NONX" =~ [yY]*) then
-			set ANS_REQ_NONX=$YES
-		else if ("$ANS_REQ_NONX" =~ [nN]*) then
-			set ANS_REQ_NONX=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_NONX=$DEF_REQ_NONX
-	endif
-
-ask_require_x_progs:
-	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
-	set ANS_REQ_X = $<
-	if ("$ANS_REQ_X" == "?") then
-		echo "* These are the programs that require X windows."
-		echo "  If you do not require all of the X programs, you should abort"
-		echo "  and manually make the ones you require."
-
-		echo ""
-		goto ask_require_x_progs
-	else if ("$ANS_REQ_X" != "") then
-		if ("$ANS_REQ_X" =~ [yY]*) then
-			set ANS_REQ_X=$YES
-		else if ("$ANS_REQ_X" =~ [nN]*) then
-			set ANS_REQ_X=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_X=$DEF_REQ_X
-	endif
-
-
-ask_require_ted:
-	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
-	set ANS_REQ_TED = $<
-	if ("$ANS_REQ_TED" == "?") then
-		echo "* This is the trace editor program.  It allows you to look at"
-		echo "  traces obtained from automated fluorescent sequencing machines."
-		echo ""
-		goto ask_require_ted
-	else if ("$ANS_REQ_TED" != "") then
-		if ("$ANS_REQ_TED" =~ [yY]*) then
-			set ANS_REQ_TED=$YES
-		else if ("$ANS_REQ_TED" =~ [nN]*) then
-			set ANS_REQ_TED=$NO
-		else
-			goto ask_require_ted
-		endif
-	else
-		set ANS_REQ_TED=$DEF_REQ_TED
-	endif
-
-
-
-ask_require_misc:
-	echo -n "Compile other programs [$DEF_REQ_MISC]? "
-	set ANS_REQ_MISC = $<
-	if ("$ANS_REQ_MISC" == "?") then
-		echo "* Other programs include:"
-		echo "    alfsplit"
-		echo "    getABISampleName"
-		echo ""
-		goto ask_require_misc
-	else if ("$ANS_REQ_MISC" != "") then
-		if ("$ANS_REQ_MISC" =~ [yY]*) then
-			set ANS_REQ_MISC=$YES
-		else if ("$ANS_REQ_MISC" =~ [nN]*) then
-			set ANS_REQ_MISC=$NO
-		else
-			goto ask_require_misc
-		endif
-	else
-		set ANS_REQ_MISC=$DEF_REQ_MISC
-	endif
-
-
-
-time_taken_warning:
-	echo ""
-	echo "The installation procedure is now ready to start."
-	echo ""
-	echo "**** Warning:"
-	echo "    The installation will take considerable time to complete.  If you"
-	echo "    are installing the whole Staden Package from scratch it could"
-	echo "    take as long as an hour for all exectuables to be compiled and"
-	echo "    installed."
-	echo ""
-
-ask_goahead:
-	echo -n "Proceed with the installation [YES]? " 
-	set ANSWER=$<
-	if ("$ANSWER" == "?") then
-		echo "* Final confirmation to proceed with the installation.  Answer"
-		echo "  YES to proceed; otherwise, answer NO to abort the installation."
-		echo ""
-		goto ask_goahead
-	else if ("$ANSWER" != "") then
-		if ("$ANSWER" =~ [nN]*) then
-			goto chickens_exit
-		else if ("$ANSWER" !~ [yY]*) then
-			goto ask_goahead
-		endif
-	endif
-
-installation_proper:
-
-# make binaries directory if it doesn't exist
-
-	if (! -d $DIR_BIN) then
-		$MKDIR $DIR_BIN
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
-		echo ""
-		echo "+ Compiling miscellaneous library"
-
-		pushd $DIR_MISC > /dev/null
-
-		cd $DIR_BINARIES
-	        $MAKE all
-
-		popd > /dev/null
-
-	endif
-
-        if ("$ANS_REQ_NONX" == "$YES") then
-		echo ""
-		echo "+ Installing non X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE nprogs lprogs
-                $INSTALL mep $DIR_BIN
-		$INSTALL nip $DIR_BIN
-		$INSTALL pip $DIR_BIN
-		$INSTALL sap $DIR_BIN
-		$INSTALL sapf $DIR_BIN
-		$INSTALL sip $DIR_BIN
-		$INSTALL splitp1 $DIR_BIN
-		$INSTALL splitp2 $DIR_BIN
-		$INSTALL splitp3 $DIR_BIN
-		$INSTALL sethelp $DIR_BIN
-		$INSTALL gip $DIR_BIN
-		$INSTALL nipl $DIR_BIN
-		$INSTALL pipl $DIR_BIN
-		$INSTALL sipl $DIR_BIN
-		$INSTALL dap $DIR_BIN
-		$INSTALL nipf $DIR_BIN
-		$INSTALL vep $DIR_BIN
-		$INSTALL rep $DIR_BIN
-		$INSTALL lip $DIR_BIN
-		#$INSTALL convert_project $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE bap
-                $INSTALL bap $DIR_BIN
-		popd > /dev/null
-
-	endif
-
-	if ("$ANS_REQ_TED" == "$YES") then
-		echo ""
-		echo "+ Installing Trace editor"
-
-		pushd $DIR_TED > /dev/null
-		cd $DIR_BINARIES
-                $MAKE ted
-		$INSTALL ted $DIR_BIN
-		popd > /dev/null
-	endif
-
-	if ("$ANS_REQ_X" == "$YES") then
-		echo ""
-		echo "+ Installing X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-                $MAKE xprogs
-		$INSTALL xmep $DIR_BIN
-		$INSTALL xnip $DIR_BIN
-		$INSTALL xpip $DIR_BIN
-		$INSTALL xsap $DIR_BIN
-		$INSTALL xsip $DIR_BIN
-		$INSTALL xdap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE xbap
-                $INSTALL xbap $DIR_BIN
-		popd > /dev/null
-
-
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES") then
-		echo ""
-		echo "+ Installing miscellaneous programs"
-
-		pushd $DIR_ABI > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL getABISampleName $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_ALF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE alfsplit
-		$INSTALL alfsplit $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_CONVERT > /dev/null
-		cd $DIR_BINARIES
-                $MAKE convert
-		$INSTALL convert $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_COP > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL cop $DIR_BIN
-		$INSTALL cop-bap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_FROG > /dev/null
-		cd $DIR_BINARIES
-                $MAKE frog
-		$INSTALL frog $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_GETMCH > /dev/null
-		cd $DIR_BINARIES
-                $MAKE trace2seq
-		$INSTALL trace2seq $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_SCF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE makeSCF
-		$INSTALL makeSCF $DIR_BIN
-		popd > /dev/null
-
-
-
-	endif
-
-
-installation_done:
-	echo ""
-	echo "+ Installation completed"
-	echo ""
-
-	echo "  Some further initialisation is required in order to use the"
-	echo "  package.  csh users should insert the following in their .login"
-	echo "  files:"
-	echo "  "
-	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
-	echo '  	source $STADENROOT/staden.login'
-	echo "  "
-	echo "  Users of the Bourne shell, sh, should insert the following in"
-	echo "  their .profile:"
-	echo "  "
-	echo "  	STADENROOT=$ANS_STADEN_ROOT"
-	echo "  	export STADENROOT"
-	echo '  	. $STADENROOT/staden.profile'
-	echo "  "
-	echo "  These initialisations will alter the shell's search path so that"
-	echo "  it can find the programs in the STADEN Package"
-	echo "  "
-
-normal_exit:
-	exit 0
-
-chickens_exit:
-	echo ""
-	echo "+ Installation cancelled"
-	echo ""
-
-	exit 0
-
-end_failure:
-	unset noglob
-	echo ""
-	echo "Aborted STADEN Package installation on `date`" 
-	echo ""
-	exit 1
-
diff --git a/Staden_install-solaris b/Staden_install-solaris
deleted file mode 100644
index 93c2feb..0000000
--- a/Staden_install-solaris
+++ /dev/null
@@ -1,453 +0,0 @@
-#! /bin/csh -f
-#
-# staden_install - version 2.4
-#
-#	This is a prototype installation program.
-#
-# 9 March 1992
-#	Modified for installation on Sun, Alliant, etc
-#	No longer install 2rs
-#
-# 20 November 1992
-#	Now includes convert, cop, frog, getMCH and scf
-#
-# 25 November 1992
-#	SGI supported
-# 
-# 19 May 1993
-#	DEC Alpha, Solaris supported
-# 
-# Written by sd@uk.ac.cam.mrc-lmb
-#
-
-# prelim
-set prog = $0 ; set prog = $prog:t
-
-# Machines supported: al sun dec sgi alpha solaris
-#set MACHINE = `echo $prog | sed 's/.*-//'`
-set MACHINE = solaris
-
-# For local (MRC-LMB) setup only
-#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
-set LOCAL = NO
-
-
-echo ""
-echo -n "Staden Package installation procedure - "
-switch (${MACHINE})
-	case "al":
-		echo "Alliant FX/2800 Concentrix version"
-		set MAKE = "make -sk"
-		breaksw
-	case "sun":
-		echo "SunOS version"
-		set MAKE = "make -sk"
-		breaksw
-	case "dec":
-		echo "DEC Ultrix (mips) version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "sgi":
-		echo "Silicon Graphics Iris version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "alpha":
-		echo "DEC Alpha OSF/1 version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "solaris":
-		echo "Solaris version"
-		set MAKE = "make -sk"
-		breaksw
-	default:
-		echo "Panic. Unknown version"
-		exit 1
-endsw
-echo ""
-echo "* starting initialization...please wait."
-echo ""
-
-# Binary fork of source directory
-if ($LOCAL == "YES") then
-    set DIR_BINARIES = ${MACHINE}-binaries
-    set DIR_PROGS = ${MACHINE}-bin
-else
-    set DIR_BINARIES = .
-    set DIR_PROGS = bin
-    set MAKE = "$MAKE -f makefile-${MACHINE}"
-endif
-
-init:
-# Set useful shell variables
-set YES="YES";
-set NO="NO"
-
-# set/unset some .cshrc envs.
-unset noclobber
-set noglob
-
-# set interrupt trap
-onintr end_failure
-
-# Make dir command
-set MKDIR = "mkdir"
-
-# Copy command
-set CP = "cp -p"
-
-# Install command
-#set INSTALL = "install"
-#set INSTALL = "mv"
-set INSTALL = "cp"
-
-# Set up default responses
-set DEF_STADEN_ROOT = `pwd`
-
-set DEF_REQ_NONX = "$YES"
-set DEF_REQ_X = "$YES"
-set DEF_REQ_TED = "$YES"
-set DEF_REQ_MISC = "$YES"
-
-# directories
-set DIR_SRC = $DEF_STADEN_ROOT/src
-set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
-set DIR_MISC = $DIR_SRC/Misc
-set DIR_STADEN = $DIR_SRC/staden
-set DIR_TED = $DIR_SRC/ted
-set DIR_ABI = $DIR_SRC/abi
-set DIR_ALF = $DIR_SRC/alf
-set DIR_BAP = $DIR_SRC/bap
-set DIR_OSP = $DIR_SRC/bap/osp-bits
-set DIR_CONVERT = $DIR_SRC/convert
-set DIR_COP = $DIR_SRC/cop
-set DIR_FROG = $DIR_SRC/frog
-set DIR_GETMCH = $DIR_SRC/getMCH
-set DIR_SCF = $DIR_SRC/scf
-
-
-main:
-
-	
-preamble:
-	echo ""
-	echo ""
-	echo "* Please answer the following questions."
-	echo "  Default answers to questions are given in square brackets."
-	echo "  If you require help at any stage respond with a ? to the question."
-	echo ""
-
-ask_staden_root:
-	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
-
-ask_require_nonx_progs: 
-	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
-	set ANS_REQ_NONX = $<
-	if ("$ANS_REQ_NONX" == "?") then
-		echo "* If you do not have X windows on your system you will require"
-		echo "  these.  However, you will require Tektronics terminal emulation."
-		echo "  If you do not require all of the non-X programs, you should abort"
-		echo "  and manually make the ones you require."
-		echo ""
-		goto ask_require_nonx_progs
-	else if ("$ANS_REQ_NONX" != "") then
-		if ("$ANS_REQ_NONX" =~ [yY]*) then
-			set ANS_REQ_NONX=$YES
-		else if ("$ANS_REQ_NONX" =~ [nN]*) then
-			set ANS_REQ_NONX=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_NONX=$DEF_REQ_NONX
-	endif
-
-ask_require_x_progs:
-	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
-	set ANS_REQ_X = $<
-	if ("$ANS_REQ_X" == "?") then
-		echo "* These are the programs that require X windows."
-		echo "  If you do not require all of the X programs, you should abort"
-		echo "  and manually make the ones you require."
-
-		echo ""
-		goto ask_require_x_progs
-	else if ("$ANS_REQ_X" != "") then
-		if ("$ANS_REQ_X" =~ [yY]*) then
-			set ANS_REQ_X=$YES
-		else if ("$ANS_REQ_X" =~ [nN]*) then
-			set ANS_REQ_X=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_X=$DEF_REQ_X
-	endif
-
-
-ask_require_ted:
-	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
-	set ANS_REQ_TED = $<
-	if ("$ANS_REQ_TED" == "?") then
-		echo "* This is the trace editor program.  It allows you to look at"
-		echo "  traces obtained from automated fluorescent sequencing machines."
-		echo ""
-		goto ask_require_ted
-	else if ("$ANS_REQ_TED" != "") then
-		if ("$ANS_REQ_TED" =~ [yY]*) then
-			set ANS_REQ_TED=$YES
-		else if ("$ANS_REQ_TED" =~ [nN]*) then
-			set ANS_REQ_TED=$NO
-		else
-			goto ask_require_ted
-		endif
-	else
-		set ANS_REQ_TED=$DEF_REQ_TED
-	endif
-
-
-
-ask_require_misc:
-	echo -n "Compile other programs [$DEF_REQ_MISC]? "
-	set ANS_REQ_MISC = $<
-	if ("$ANS_REQ_MISC" == "?") then
-		echo "* Other programs include:"
-		echo "    alfsplit"
-		echo "    getABISampleName"
-		echo ""
-		goto ask_require_misc
-	else if ("$ANS_REQ_MISC" != "") then
-		if ("$ANS_REQ_MISC" =~ [yY]*) then
-			set ANS_REQ_MISC=$YES
-		else if ("$ANS_REQ_MISC" =~ [nN]*) then
-			set ANS_REQ_MISC=$NO
-		else
-			goto ask_require_misc
-		endif
-	else
-		set ANS_REQ_MISC=$DEF_REQ_MISC
-	endif
-
-
-
-time_taken_warning:
-	echo ""
-	echo "The installation procedure is now ready to start."
-	echo ""
-	echo "**** Warning:"
-	echo "    The installation will take considerable time to complete.  If you"
-	echo "    are installing the whole Staden Package from scratch it could"
-	echo "    take as long as an hour for all exectuables to be compiled and"
-	echo "    installed."
-	echo ""
-
-ask_goahead:
-	echo -n "Proceed with the installation [YES]? " 
-	set ANSWER=$<
-	if ("$ANSWER" == "?") then
-		echo "* Final confirmation to proceed with the installation.  Answer"
-		echo "  YES to proceed; otherwise, answer NO to abort the installation."
-		echo ""
-		goto ask_goahead
-	else if ("$ANSWER" != "") then
-		if ("$ANSWER" =~ [nN]*) then
-			goto chickens_exit
-		else if ("$ANSWER" !~ [yY]*) then
-			goto ask_goahead
-		endif
-	endif
-
-installation_proper:
-
-# make binaries directory if it doesn't exist
-
-	if (! -d $DIR_BIN) then
-		$MKDIR $DIR_BIN
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
-		echo ""
-		echo "+ Compiling miscellaneous library"
-
-		pushd $DIR_MISC > /dev/null
-
-		cd $DIR_BINARIES
-	        $MAKE all
-
-		popd > /dev/null
-
-	endif
-
-        if ("$ANS_REQ_NONX" == "$YES") then
-		echo ""
-		echo "+ Installing non X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE nprogs lprogs
-                $INSTALL mep $DIR_BIN
-		$INSTALL nip $DIR_BIN
-		$INSTALL pip $DIR_BIN
-		$INSTALL sap $DIR_BIN
-		$INSTALL sapf $DIR_BIN
-		$INSTALL sip $DIR_BIN
-		$INSTALL splitp1 $DIR_BIN
-		$INSTALL splitp2 $DIR_BIN
-		$INSTALL splitp3 $DIR_BIN
-		$INSTALL sethelp $DIR_BIN
-		$INSTALL gip $DIR_BIN
-		$INSTALL nipl $DIR_BIN
-		$INSTALL pipl $DIR_BIN
-		$INSTALL sipl $DIR_BIN
-		$INSTALL dap $DIR_BIN
-		$INSTALL nipf $DIR_BIN
-		$INSTALL vep $DIR_BIN
-		$INSTALL rep $DIR_BIN
-		$INSTALL lip $DIR_BIN
-		#$INSTALL convert_project $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE bap
-                $INSTALL bap $DIR_BIN
-		popd > /dev/null
-
-	endif
-
-	if ("$ANS_REQ_TED" == "$YES") then
-		echo ""
-		echo "+ Installing Trace editor"
-
-		pushd $DIR_TED > /dev/null
-		cd $DIR_BINARIES
-                $MAKE ted
-		$INSTALL ted $DIR_BIN
-		popd > /dev/null
-	endif
-
-	if ("$ANS_REQ_X" == "$YES") then
-		echo ""
-		echo "+ Installing X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-                $MAKE xprogs
-		$INSTALL xmep $DIR_BIN
-		$INSTALL xnip $DIR_BIN
-		$INSTALL xpip $DIR_BIN
-		$INSTALL xsap $DIR_BIN
-		$INSTALL xsip $DIR_BIN
-		$INSTALL xdap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE xbap
-                $INSTALL xbap $DIR_BIN
-		popd > /dev/null
-
-
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES") then
-		echo ""
-		echo "+ Installing miscellaneous programs"
-
-		pushd $DIR_ABI > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL getABISampleName $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_ALF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE alfsplit
-		$INSTALL alfsplit $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_CONVERT > /dev/null
-		cd $DIR_BINARIES
-                $MAKE convert
-		$INSTALL convert $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_COP > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL cop $DIR_BIN
-		$INSTALL cop-bap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_FROG > /dev/null
-		cd $DIR_BINARIES
-                $MAKE frog
-		$INSTALL frog $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_GETMCH > /dev/null
-		cd $DIR_BINARIES
-                $MAKE trace2seq
-		$INSTALL trace2seq $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_SCF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE makeSCF
-		$INSTALL makeSCF $DIR_BIN
-		popd > /dev/null
-
-
-
-	endif
-
-
-installation_done:
-	echo ""
-	echo "+ Installation completed"
-	echo ""
-
-	echo "  Some further initialisation is required in order to use the"
-	echo "  package.  csh users should insert the following in their .login"
-	echo "  files:"
-	echo "  "
-	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
-	echo '  	source $STADENROOT/staden.login'
-	echo "  "
-	echo "  Users of the Bourne shell, sh, should insert the following in"
-	echo "  their .profile:"
-	echo "  "
-	echo "  	STADENROOT=$ANS_STADEN_ROOT"
-	echo "  	export STADENROOT"
-	echo '  	. $STADENROOT/staden.profile'
-	echo "  "
-	echo "  These initialisations will alter the shell's search path so that"
-	echo "  it can find the programs in the STADEN Package"
-	echo "  "
-
-normal_exit:
-	exit 0
-
-chickens_exit:
-	echo ""
-	echo "+ Installation cancelled"
-	echo ""
-
-	exit 0
-
-end_failure:
-	unset noglob
-	echo ""
-	echo "Aborted STADEN Package installation on `date`" 
-	echo ""
-	exit 1
-
diff --git a/Staden_install-sun b/Staden_install-sun
deleted file mode 100644
index 0d6711e..0000000
--- a/Staden_install-sun
+++ /dev/null
@@ -1,453 +0,0 @@
-#! /bin/csh -f
-#
-# staden_install - version 2.4
-#
-#	This is a prototype installation program.
-#
-# 9 March 1992
-#	Modified for installation on Sun, Alliant, etc
-#	No longer install 2rs
-#
-# 20 November 1992
-#	Now includes convert, cop, frog, getMCH and scf
-#
-# 25 November 1992
-#	SGI supported
-# 
-# 19 May 1993
-#	DEC Alpha, Solaris supported
-# 
-# Written by sd@uk.ac.cam.mrc-lmb
-#
-
-# prelim
-set prog = $0 ; set prog = $prog:t
-
-# Machines supported: al sun dec sgi alpha solaris
-#set MACHINE = `echo $prog | sed 's/.*-//'`
-set MACHINE = sun
-
-# For local (MRC-LMB) setup only
-#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
-set LOCAL = NO
-
-
-echo ""
-echo -n "Staden Package installation procedure - "
-switch (${MACHINE})
-	case "al":
-		echo "Alliant FX/2800 Concentrix version"
-		set MAKE = "make -sk"
-		breaksw
-	case "sun":
-		echo "SunOS version"
-		set MAKE = "make -sk"
-		breaksw
-	case "dec":
-		echo "DEC Ultrix (mips) version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "sgi":
-		echo "Silicon Graphics Iris version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "alpha":
-		echo "DEC Alpha OSF/1 version"
-		set MAKE = "gmake -sk"
-		breaksw
-	case "solaris":
-		echo "Solaris version"
-		set MAKE = "make -sk"
-		breaksw
-	default:
-		echo "Panic. Unknown version"
-		exit 1
-endsw
-echo ""
-echo "* starting initialization...please wait."
-echo ""
-
-# Binary fork of source directory
-if ($LOCAL == "YES") then
-    set DIR_BINARIES = ${MACHINE}-binaries
-    set DIR_PROGS = ${MACHINE}-bin
-else
-    set DIR_BINARIES = .
-    set DIR_PROGS = bin
-    set MAKE = "$MAKE -f makefile-${MACHINE}"
-endif
-
-init:
-# Set useful shell variables
-set YES="YES";
-set NO="NO"
-
-# set/unset some .cshrc envs.
-unset noclobber
-set noglob
-
-# set interrupt trap
-onintr end_failure
-
-# Make dir command
-set MKDIR = "mkdir"
-
-# Copy command
-set CP = "cp -p"
-
-# Install command
-#set INSTALL = "install"
-#set INSTALL = "mv"
-set INSTALL = "cp"
-
-# Set up default responses
-set DEF_STADEN_ROOT = `pwd`
-
-set DEF_REQ_NONX = "$YES"
-set DEF_REQ_X = "$YES"
-set DEF_REQ_TED = "$YES"
-set DEF_REQ_MISC = "$YES"
-
-# directories
-set DIR_SRC = $DEF_STADEN_ROOT/src
-set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
-set DIR_MISC = $DIR_SRC/Misc
-set DIR_STADEN = $DIR_SRC/staden
-set DIR_TED = $DIR_SRC/ted
-set DIR_ABI = $DIR_SRC/abi
-set DIR_ALF = $DIR_SRC/alf
-set DIR_BAP = $DIR_SRC/bap
-set DIR_OSP = $DIR_SRC/bap/osp-bits
-set DIR_CONVERT = $DIR_SRC/convert
-set DIR_COP = $DIR_SRC/cop
-set DIR_FROG = $DIR_SRC/frog
-set DIR_GETMCH = $DIR_SRC/getMCH
-set DIR_SCF = $DIR_SRC/scf
-
-
-main:
-
-	
-preamble:
-	echo ""
-	echo ""
-	echo "* Please answer the following questions."
-	echo "  Default answers to questions are given in square brackets."
-	echo "  If you require help at any stage respond with a ? to the question."
-	echo ""
-
-ask_staden_root:
-	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
-
-ask_require_nonx_progs: 
-	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
-	set ANS_REQ_NONX = $<
-	if ("$ANS_REQ_NONX" == "?") then
-		echo "* If you do not have X windows on your system you will require"
-		echo "  these.  However, you will require Tektronics terminal emulation."
-		echo "  If you do not require all of the non-X programs, you should abort"
-		echo "  and manually make the ones you require."
-		echo ""
-		goto ask_require_nonx_progs
-	else if ("$ANS_REQ_NONX" != "") then
-		if ("$ANS_REQ_NONX" =~ [yY]*) then
-			set ANS_REQ_NONX=$YES
-		else if ("$ANS_REQ_NONX" =~ [nN]*) then
-			set ANS_REQ_NONX=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_NONX=$DEF_REQ_NONX
-	endif
-
-ask_require_x_progs:
-	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
-	set ANS_REQ_X = $<
-	if ("$ANS_REQ_X" == "?") then
-		echo "* These are the programs that require X windows."
-		echo "  If you do not require all of the X programs, you should abort"
-		echo "  and manually make the ones you require."
-
-		echo ""
-		goto ask_require_x_progs
-	else if ("$ANS_REQ_X" != "") then
-		if ("$ANS_REQ_X" =~ [yY]*) then
-			set ANS_REQ_X=$YES
-		else if ("$ANS_REQ_X" =~ [nN]*) then
-			set ANS_REQ_X=$NO
-		else
-			goto ask_require_nonx_progs
-		endif
-	else
-		set ANS_REQ_X=$DEF_REQ_X
-	endif
-
-
-ask_require_ted:
-	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
-	set ANS_REQ_TED = $<
-	if ("$ANS_REQ_TED" == "?") then
-		echo "* This is the trace editor program.  It allows you to look at"
-		echo "  traces obtained from automated fluorescent sequencing machines."
-		echo ""
-		goto ask_require_ted
-	else if ("$ANS_REQ_TED" != "") then
-		if ("$ANS_REQ_TED" =~ [yY]*) then
-			set ANS_REQ_TED=$YES
-		else if ("$ANS_REQ_TED" =~ [nN]*) then
-			set ANS_REQ_TED=$NO
-		else
-			goto ask_require_ted
-		endif
-	else
-		set ANS_REQ_TED=$DEF_REQ_TED
-	endif
-
-
-
-ask_require_misc:
-	echo -n "Compile other programs [$DEF_REQ_MISC]? "
-	set ANS_REQ_MISC = $<
-	if ("$ANS_REQ_MISC" == "?") then
-		echo "* Other programs include:"
-		echo "    alfsplit"
-		echo "    getABISampleName"
-		echo ""
-		goto ask_require_misc
-	else if ("$ANS_REQ_MISC" != "") then
-		if ("$ANS_REQ_MISC" =~ [yY]*) then
-			set ANS_REQ_MISC=$YES
-		else if ("$ANS_REQ_MISC" =~ [nN]*) then
-			set ANS_REQ_MISC=$NO
-		else
-			goto ask_require_misc
-		endif
-	else
-		set ANS_REQ_MISC=$DEF_REQ_MISC
-	endif
-
-
-
-time_taken_warning:
-	echo ""
-	echo "The installation procedure is now ready to start."
-	echo ""
-	echo "**** Warning:"
-	echo "    The installation will take considerable time to complete.  If you"
-	echo "    are installing the whole Staden Package from scratch it could"
-	echo "    take as long as an hour for all exectuables to be compiled and"
-	echo "    installed."
-	echo ""
-
-ask_goahead:
-	echo -n "Proceed with the installation [YES]? " 
-	set ANSWER=$<
-	if ("$ANSWER" == "?") then
-		echo "* Final confirmation to proceed with the installation.  Answer"
-		echo "  YES to proceed; otherwise, answer NO to abort the installation."
-		echo ""
-		goto ask_goahead
-	else if ("$ANSWER" != "") then
-		if ("$ANSWER" =~ [nN]*) then
-			goto chickens_exit
-		else if ("$ANSWER" !~ [yY]*) then
-			goto ask_goahead
-		endif
-	endif
-
-installation_proper:
-
-# make binaries directory if it doesn't exist
-
-	if (! -d $DIR_BIN) then
-		$MKDIR $DIR_BIN
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
-		echo ""
-		echo "+ Compiling miscellaneous library"
-
-		pushd $DIR_MISC > /dev/null
-
-		cd $DIR_BINARIES
-	        $MAKE all
-
-		popd > /dev/null
-
-	endif
-
-        if ("$ANS_REQ_NONX" == "$YES") then
-		echo ""
-		echo "+ Installing non X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE nprogs lprogs
-                $INSTALL mep $DIR_BIN
-		$INSTALL nip $DIR_BIN
-		$INSTALL pip $DIR_BIN
-		$INSTALL sap $DIR_BIN
-		$INSTALL sapf $DIR_BIN
-		$INSTALL sip $DIR_BIN
-		$INSTALL splitp1 $DIR_BIN
-		$INSTALL splitp2 $DIR_BIN
-		$INSTALL splitp3 $DIR_BIN
-		$INSTALL sethelp $DIR_BIN
-		$INSTALL gip $DIR_BIN
-		$INSTALL nipl $DIR_BIN
-		$INSTALL pipl $DIR_BIN
-		$INSTALL sipl $DIR_BIN
-		$INSTALL dap $DIR_BIN
-		$INSTALL nipf $DIR_BIN
-		$INSTALL vep $DIR_BIN
-		$INSTALL rep $DIR_BIN
-		$INSTALL lip $DIR_BIN
-		#$INSTALL convert_project $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE bap
-                $INSTALL bap $DIR_BIN
-		popd > /dev/null
-
-	endif
-
-	if ("$ANS_REQ_TED" == "$YES") then
-		echo ""
-		echo "+ Installing Trace editor"
-
-		pushd $DIR_TED > /dev/null
-		cd $DIR_BINARIES
-                $MAKE ted
-		$INSTALL ted $DIR_BIN
-		popd > /dev/null
-	endif
-
-	if ("$ANS_REQ_X" == "$YES") then
-		echo ""
-		echo "+ Installing X programs"
-
-		pushd $DIR_STADEN > /dev/null
-		cd $DIR_BINARIES
-                $MAKE xprogs
-		$INSTALL xmep $DIR_BIN
-		$INSTALL xnip $DIR_BIN
-		$INSTALL xpip $DIR_BIN
-		$INSTALL xsap $DIR_BIN
-		$INSTALL xsip $DIR_BIN
-		$INSTALL xdap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_OSP > /dev/null
-		cd $DIR_BINARIES
-		$MAKE
-		popd > /dev/null		
-
-		pushd $DIR_BAP > /dev/null
-		cd $DIR_BINARIES
-	        $MAKE xbap
-                $INSTALL xbap $DIR_BIN
-		popd > /dev/null
-
-
-	endif
-
-	if ("$ANS_REQ_MISC" == "$YES") then
-		echo ""
-		echo "+ Installing miscellaneous programs"
-
-		pushd $DIR_ABI > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL getABISampleName $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_ALF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE alfsplit
-		$INSTALL alfsplit $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_CONVERT > /dev/null
-		cd $DIR_BINARIES
-                $MAKE convert
-		$INSTALL convert $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_COP > /dev/null
-		cd $DIR_BINARIES
-                $MAKE all
-		$INSTALL cop $DIR_BIN
-		$INSTALL cop-bap $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_FROG > /dev/null
-		cd $DIR_BINARIES
-                $MAKE frog
-		$INSTALL frog $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_GETMCH > /dev/null
-		cd $DIR_BINARIES
-                $MAKE trace2seq
-		$INSTALL trace2seq $DIR_BIN
-		popd > /dev/null
-
-		pushd $DIR_SCF > /dev/null
-		cd $DIR_BINARIES
-                $MAKE makeSCF
-		$INSTALL makeSCF $DIR_BIN
-		popd > /dev/null
-
-
-
-	endif
-
-
-installation_done:
-	echo ""
-	echo "+ Installation completed"
-	echo ""
-
-	echo "  Some further initialisation is required in order to use the"
-	echo "  package.  csh users should insert the following in their .login"
-	echo "  files:"
-	echo "  "
-	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
-	echo '  	source $STADENROOT/staden.login'
-	echo "  "
-	echo "  Users of the Bourne shell, sh, should insert the following in"
-	echo "  their .profile:"
-	echo "  "
-	echo "  	STADENROOT=$ANS_STADEN_ROOT"
-	echo "  	export STADENROOT"
-	echo '  	. $STADENROOT/staden.profile'
-	echo "  "
-	echo "  These initialisations will alter the shell's search path so that"
-	echo "  it can find the programs in the STADEN Package"
-	echo "  "
-
-normal_exit:
-	exit 0
-
-chickens_exit:
-	echo ""
-	echo "+ Installation cancelled"
-	echo ""
-
-	exit 0
-
-end_failure:
-	unset noglob
-	echo ""
-	echo "Aborted STADEN Package installation on `date`" 
-	echo ""
-	exit 1
-