X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fbinaries%2Fmafft;fp=binaries%2Fsrc%2Fmafft%2Fbinaries%2Fmafft;h=0000000000000000000000000000000000000000;hb=6e0ce943f09b5ac30f3eb8dc0f20bc75114669ce;hp=93578e733e5463596d304fdff0ecfa6fffea136d;hpb=48f0451143441afce738d887b0cde1fb5cdbc02e;p=jabaws.git

diff --git a/binaries/src/mafft/binaries/mafft b/binaries/src/mafft/binaries/mafft
deleted file mode 100644
index 93578e7..0000000
--- a/binaries/src/mafft/binaries/mafft
+++ /dev/null
@@ -1,1533 +0,0 @@
-#! /bin/sh
-
-
-er=0;
-myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v6.717b (2009/12/03)"; export version
-LANG=C; export LANG
-os=`uname`
-progname=`basename "$0"`
-if [ `echo $os | grep -i cygwin` ]; then
-	os="cygwin"
-elif [ `echo $os | grep -i darwin` ]; then
-	os="darwin"
-elif [ `echo $os | grep -i sunos` ]; then
-	os="sunos"
-else
-	os="unix"
-fi
-export os
-
-if [ "$MAFFT_BINARIES" ]; then
-	prefix="$MAFFT_BINARIES"
-else
-	prefix=/usr/lib/mafft
-fi
-export prefix
-
-if [ $# -gt 0 ]; then
-	if [ "$1" = "--man" ]; then 
-		man "$prefix/mafft.1"
-		exit 0;
-	fi
-fi
-
-if [ ! -x "$prefix/tbfast" ]; then
-	echo "" 1>&2
-	echo "correctly installed?" 1>&2
-	echo "mafft binaries have to be installed in \$MAFFT_BINARIES" 1>&2
-	echo "or the $prefix directory". 1>&2
-	echo "" 1>&2
-	exit 1
-	er=1
-fi
-
-defaultiterate=0
-defaultcycle=2
-defaultgop="1.53"
-#defaultaof="0.123"
-defaultaof="0.000"
-defaultlaof="0.100"
-defaultlgop="-2.00"
-defaultfft=1
-defaultrough=0
-defaultdistance="sixtuples"
-#defaultdistance="local"
-defaultweighti="2.7"
-defaultweightr="0.0"
-defaultweightm="1.0"
-defaultmccaskill=0
-defaultcontrafold=0
-defaultalgopt="  "
-defaultalgoptit="  "
-defaultsbstmodel=" -b 62 "
-defaultfmodel=" "
-defaultkappa=" "
-if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then
-	defaultfft=1
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="scarna"
-	defaultweighti="3.2"
-	defaultweightr="8.0"
-	defaultweightm="2.0"
-	defaultmccaskill=1
-	defaultcontrafold=0
-	defaultalgopt=" -A "
-	defaultalgoptit=" -AB " ## chui
-	defaultaof="0.0"
-	defaultsbstmodel=" -b 62 "
-	defaultkappa=" "
-	defaultfmodel=" -a "
-elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
-	defaultfft=1
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="global"
-	defaultweighti="3.2"
-	defaultweightr="8.0"
-	defaultweightm="2.0"
-	defaultmccaskill=1
-	defaultcontrafold=0
-	defaultalgopt=" -A "
-	defaultalgoptit=" -AB " ## chui
-	defaultaof="0.0"
-	defaultsbstmodel=" -b 62 "
-	defaultkappa=" "
-	defaultfmodel=" -a "
-elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
-	defaultfft=0
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="local"
-elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then
-	defaultfft=1
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="global"
-elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then
-	defaultfft=0
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="localgenaf"
-elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
-	defaultfft=1
-	defaultcycle=2
-	defaultdistance="sixtuples"
-elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
-	defaultfft=1
-	defaultcycle=2
-	defaultiterate=2
-	defaultdistance="sixtuples"
-elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
-	defaultfft=0
-	defaultcycle=2
-	defaultdistance="sixtuples"
-elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
-	defaultfft=0
-	defaultcycle=2
-	defaultiterate=2
-	defaultdistance="sixtuples"
-fi
-kappa=$defaultkappa
-sbstmodel=$defaultsbstmodel
-fmodel=$defaultfmodel
-gop=$defaultgop
-aof=$defaultaof
-cycle=$defaultcycle
-iterate=$defaultiterate
-fft=$defaultfft
-rough=$defaultrough
-distance=$defaultdistance
-forcefft=0
-memopt=" "
-weightopt=" "
-GGOP="-6.00"
-LGOP="-6.00"
-LEXP="-0.000"
-GEXP="-0.000"
-lgop=$defaultlgop
-lexp="-0.100"
-laof=$defaultlaof
-pggop="-2.00"
-pgexp="-0.10"
-pgaof="0.10"
-rgop="-1.530"
-rgep="-0.000"
-seqtype="  "
-weighti=$defaultweighti
-weightr=$defaultweightr
-weightm=$defaultweightm
-rnaalifold=0
-mccaskill=$defaultmccaskill
-contrafold=$defaultcontrafold
-quiet=0
-debug=0
-sw=0
-algopt=$defaultalgopt
-algoptit=$defaultalgoptit
-scorecalcopt=" "
-coreout=0
-corethr="0.5"
-corewin="100"
-coreext=" "
-outputformat="pir"
-outorder="input"
-seed="x"
-seedtable="x"
-auto=0
-groupsize=-1
-partsize=50
-partdist="sixtuples"
-partorderopt=" -x "
-treeout=0
-distout=0
-treein=0
-topin=0
-treeinopt="  "
-seedfiles="/dev/null"
-seedtablefile="/dev/null"
-aamatrix="/dev/null"
-treeinfile="/dev/null"
-rnascoremtx=" "
-laraparams="/dev/null"
-foldalignopt=" "
-treealg=" -X "
-if [ $# -gt 0 ]; then
-	while [ $# -gt 1 ];
-	do
-		if [ "$1" = "--auto" ]; then 
-			auto=1
-		elif [ "$1" = "--clustalout" ]; then 
-			outputformat="clustal"
-		elif [ "$1" = "--reorder" ]; then 
-			outorder="aligned"
-			partorderopt=" "
-		elif [ "$1" = "--inputorder" ]; then 
-			outorder="input"
-			partorderopt=" -x "
-		elif [ "$1" = "--unweight" ]; then 
-			weightopt=" -u "
-		elif [ "$1" = "--algq" ]; then 
-			algopt=" -Q "
-			algoptit=" -QB "
-		elif [ "$1" = "--groupsize" ]; then 
-			shift   
-			groupsize=`expr "$1" - 0`
-		elif [ "$1" = "--partsize" ]; then 
-			shift   
-			partsize=`expr "$1" - 0`
-		elif [ "$1" = "--parttree" ]; then 
-			distance="parttree"
-			partdist="sixtuples"
-		elif [ "$1" = "--dpparttree" ]; then 
-			distance="parttree"
-			partdist="localalign"
-		elif [ "$1" = "--fastaparttree" ]; then 
-			distance="parttree"
-			partdist="fasta"
-		elif [ "$1" = "--treeout" ]; then 
-			treeout=1
-		elif [ "$1" = "--distout" ]; then 
-			distout=1
-		elif [ "$1" = "--fastswpair" ]; then
-			distance="fasta"
-			sw=1
-		elif [ "$1" = "--fastapair" ]; then
-			distance="fasta"
-			sw=0
-		elif [ "$1" = "--averagelinkage" ]; then
-			treealg=" -E "
-		elif [ "$1" = "--minimumlinkage" ]; then
-			treealg=" -q "
-		elif [ "$1" = "--noscore" ]; then
-			scorecalcopt=" -Z "
-		elif [ "$1" = "--6merpair" ]; then
-			distance="sixtuples"
-		elif [ "$1" = "--blastpair" ]; then
-			distance="blast"
-		elif [ "$1" = "--globalpair" ]; then
-			distance="global"
-		elif [ "$1" = "--localpair" ]; then
-			distance="local"
-		elif [ "$1" = "--scarnapair" ]; then
-			distance="scarna"
-		elif [ "$1" = "--larapair" ]; then
-			distance="lara"
-		elif [ "$1" = "--slarapair" ]; then
-			distance="slara"
-		elif [ "$1" = "--foldalignpair" ]; then
-			distance="foldalignlocal"
-		elif [ "$1" = "--foldalignlocalpair" ]; then
-			distance="foldalignlocal"
-		elif [ "$1" = "--foldalignglobalpair" ]; then
-			distance="foldalignglobal"
-		elif [ "$1" = "--globalgenafpair" ]; then
-			distance="globalgenaf"
-		elif [ "$1" = "--localgenafpair" ]; then
-			distance="localgenaf"
-		elif [ "$1" = "--genafpair" ]; then
-			distance="localgenaf"
-		elif [ "$1" = "--memsave" ]; then
-			memopt=" -M -B "         # -B (bunkatsunashi no riyu ga omoidasenai)
-		elif [ "$1" = "--nomemsave" ]; then
-			memopt=" -N "
-		elif [ "$1" = "--nuc" ]; then 
-			seqtype=" -D "
-		elif [ "$1" = "--amino" ]; then 
-			seqtype=" -P "
-		elif [ "$1" = "--fft" ]; then 
-			fft=1
-			forcefft=1
-		elif [ "$1" = "--nofft" ]; then 
-			fft=0
-		elif [ "$1" = "--quiet" ]; then 
-			quiet=1
-		elif [ "$1" = "--debug" ]; then 
-			debug=1
-		elif [ "$1" = "--coreext" ]; then 
-			coreext=" -c "
-		elif [ "$1" = "--core" ]; then 
-			coreout=1
-		elif [ "$1" = "--maxiterate" ]; then 
-			shift   
-			iterate=`expr "$1" - 0` 
-		elif [ "$1" = "--retree" ]; then 
-			shift   
-			cycle=`expr "$1" - 0`
-		elif [ "$1" = "--aamatrix" ]; then 
-			shift   
-			sbstmodel=" -b -1 "
-			aamatrix="$1"
-		elif [ "$1" = "--treein" ]; then 
-			shift   
-			treeinopt=" -U "
-			treein=1
-			treeinfile="$1"
-		elif [ "$1" = "--topin" ]; then 
-			shift   
-			treeinopt=" -V "
-			treein=1
-			treeinfile="$1"
-			echo "The --topin option has been disabled." 1>&2
-			echo "There was a bug in version < 6.530."   1>&2
-			echo "This bug has not yet been fixed."      1>&2
-			exit 1
-		elif [ "$1" = "--kappa" ]; then 
-			shift   
-			kappa=" -k $1 "
-		elif [ "$1" = "--fmodel" ]; then 
-			fmodel=" -a "
-		elif [ "$1" = "--jtt" ]; then 
-			shift   
-			sbstmodel=" -j $1"
-		elif [ "$1" = "--kimura" ]; then 
-			shift   
-			sbstmodel=" -j $1"
-		elif [ "$1" = "--tm" ]; then 
-			shift   
-			sbstmodel=" -m $1"
-		elif [ "$1" = "--bl" ]; then 
-			shift   
-			sbstmodel=" -b $1"
-		elif [ "$1" = "--weighti" ]; then
-			shift   
-			weighti="$1"
-		elif [ "$1" = "--weightr" ]; then
-			shift   
-			weightr="$1"
-		elif [ "$1" = "--weightm" ]; then
-			shift   
-			weightm="$1"
-		elif [ "$1" = "--rnaalifold" ]; then
-			rnaalifold=1
-		elif [ "$1" = "--mccaskill" ]; then
-			mccaskill=1
-			contrafold=0
-		elif [ "$1" = "--contrafold" ]; then
-			mccaskill=0
-			contrafold=1
-		elif [ "$1" = "--ribosum" ]; then
-			rnascoremtx=" -s "
-		elif [ "$1" = "--op" ]; then 
-			shift   
-			gop="$1"
-		elif [ "$1" = "--ep" ]; then 
-			shift   
-			aof="$1"
-		elif [ "$1" = "--rop" ]; then 
-			shift   
-			rgop="$1"
-		elif [ "$1" = "--rep" ]; then 
-			shift   
-			rgep="$1"
-		elif [ "$1" = "--lop" ]; then 
-			shift   
-			lgop="$1"
-		elif [ "$1" = "--LOP" ]; then 
-			shift   
-			LGOP="$1"
-		elif [ "$1" = "--lep" ]; then 
-			shift   
-			laof="$1"
-		elif [ "$1" = "--lexp" ]; then 
-			shift   
-			lexp="$1"
-		elif [ "$1" = "--LEXP" ]; then 
-			shift   
-			LEXP="$1"
-		elif [ "$1" = "--GEXP" ]; then 
-			shift   
-			GEXP="$1"
-		elif [ "$1" = "--GOP" ]; then 
-			shift   
-			GGOP="$1"
-		elif [ "$1" = "--gop" ]; then 
-			shift   
-			pggop="$1"
-		elif [ "$1" = "--gep" ]; then 
-			shift   
-			pgaof="$1"
-		elif [ "$1" = "--gexp" ]; then 
-			shift   
-			pgexp="$1"
-		elif [ "$1" = "--laraparams" ]; then 
-			shift   
-			laraparams="$1"
-		elif [ "$1" = "--corethr" ]; then 
-			shift   
-			corethr="$1"
-		elif [ "$1" = "--corewin" ]; then 
-			shift   
-			corewin="$1"
-		elif [ "$1" = "--seedtable" ]; then
-			shift
-			seedtable="y"
-			seedtablefile="$1"
-		elif [ "$1" = "--seed" ]; then
-			shift
-			seed="m"
-			seedfiles="$seedfiles $1"
-		elif [ $progname = "fftns" -o  $progname = "nwns" ]; then
-			if [ "$1" -gt 0 ]; then
-				cycle=`expr "$1" - 0`
-			fi
-		else
-			echo "Unknown option:  $1" 1>&2
-			er=1;
-		fi
-		shift   
-	done;
-
-
-
-#	TMPFILE=/tmp/$progname.$$
-	TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`
-	if [ $? -ne 0 ]; then
-		echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
-		TMPFILE=`mktemp -d /tmp/$progname.XXXXXXXXXX`
-	fi	
-	umask 077
-#	mkdir  $TMPFILE  || er=1
-	if [ $debug -eq 1 ]; then
-		trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0
-	else
-		trap "rm -rf $TMPFILE " 0
-	fi
-	if [ $# -eq 1 ]; then
-		if [ -r "$1" -o "$1" = - ]; then
-			cat "$1" | tr "\r" "\n" > $TMPFILE/infile 
-			cat "$aamatrix"       | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_aamtx
-			cat "$treeinfile"     | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_guidetree
-			cat "$seedtablefile"  | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_seedtablefile
-			cat "$laraparams"     | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_lara.params
-#			echo $seedfiles
-			infilename="$1"
-			seedfilesintmp="/dev/null"
-			seednseq="0"
-			set $seedfiles > /dev/null
-			while [ $# -gt 1 ];
-			do
-				shift
-				cat "$1" | tr "\r" "\n" >  $TMPFILE/seed$#
-				seednseq=$seednseq" "`grep -c '^[>|=]' $TMPFILE/seed$#`
-				seedfilesintmp=$seedfilesintmp" "seed$#
-			done
-#			ls $TMPFILE
-#			echo $seedfilesintmp
-#			echo $seednseq
-		else
-			echo "$0": Cannot open "$1". 1>&2
-			er=1
-#			exit 1;
-		fi
-	else
-		echo '$#'"=$#" 1>&2
-		er=1
-	fi
-
-
-	if [ $auto -eq 1 ]; then
-		"$prefix/countlen" < $TMPFILE/infile > $TMPFILE/size
-		nseq=`awk '{print $1}' $TMPFILE/size`
-		nlen=`awk '{print $3}' $TMPFILE/size`
-		if [ $nlen -lt 2000 -a $nseq -lt 100 ]; then
-			distance="local"
-			iterate=1000
-		elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
-			distance="sixtuples"
-			iterate=2
-		else
-			distance="sixtuples"
-			iterate=0
-		fi
-		if [ $quiet -eq 0 ]; then
-			echo "nseq = " $nseq              1>&2
-			echo "nlen = " $nlen              1>&2
-			echo "distance = " $distance      1>&2
-			echo "iterate = " $iterate        1>&2
-		fi
-	fi
-
-	if [ $iterate -gt 16 ]; then    #??
-		iterate=16
-	fi
-
-	if [ $rnaalifold -eq 1 ]; then
-		rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx "
-#		rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R "
-		rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R "
-	elif [ $mccaskill -eq 1 -o $contrafold -eq 1 ]; then
-		rnaopt=" -o $rgop -c $weightm -r $weightr "
-#		rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx "
-		rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx "
-	else
-		rnaopt="  "
-		rnaoptit=" -F "
-	fi
-
-	model="$sbstmodel $kappa $fmodel"
-
-	if [ $er -eq 1 ]; then
-		echo "------------------------------------------------------------------------------" 1>&2
-		echo "  MAFFT" $version 1>&2
-#		echo "" 1>&2
-#		echo "  Input format: fasta" 1>&2
-#		echo ""  1>&2
-#		echo "  Usage: `basename $0` [options] inputfile > outputfile" 1>&2
-	    echo "  http://align.bmr.kyushu-u.ac.jp/mafft/software/" 1>&2
-		echo "  NAR 30:3059-3066 (2002), Briefings in Bioinformatics 9:286-298 (2008)"        1>&2
-#		echo "------------------------------------------------------------------------------" 1>&2
-#		echo "  % mafft in > out" 1>&2
-		echo "------------------------------------------------------------------------------" 1>&2
-#		echo ""  1>&2
-		echo "High speed:" 1>&2
-		echo "  % mafft in > out" 1>&2
-		echo "  % mafft --retree 1 in > out (fastest)" 1>&2
-		echo "" 1>&2
-		echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2
-		echo "  % mafft --maxiterate 1000 --localpair  in > out (% linsi in > out is also ok)" 1>&2
-		echo "  % mafft --maxiterate 1000 --genafpair  in > out (% einsi in > out)" 1>&2
-		echo "  % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2
-		echo "" 1>&2
-		echo "If unsure which option to use:" 1>&2
-		echo "  % mafft --auto in > out" 1>&2
-		echo "" 1>&2
-#		echo "Other options:" 1>&2
-		echo "--op # :         Gap opening penalty, default: 1.53" 1>&2
-		echo "--ep # :         Offset (works like gap extension penalty), default: 0.0" 1>&2
-		echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 1>&2
-		echo "--clustalout :   Output: clustal format, default: fasta" 1>&2
-		echo "--reorder :      Outorder: aligned, default: input order" 1>&2
-		echo "--quiet :        Do not report progress" 1>&2
-#		echo "" 1>&2
-#		echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2
-#		echo " most accurate in many cases, assumes only one alignable domain" 1>&2 
-#		echo "" 1>&2
-#		echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2
-#		echo " works well if many unalignable residues exist between alignable domains" 1>&2
-#		echo "" 1>&2
-#		echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2
-#		echo " suitable for globally alignable sequences            " 1>&2
-#		echo "" 1>&2
-#		echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2
-#		echo " accurate and slow, iterative refinement method      " 1>&2
-#		echo "" 1>&2
-#		echo "If the input sequences are long (~1,000,000nt)," 1>&2
-#		echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2
-#		echo "" 1>&2
-#		echo "If many (~5,000) sequences are to be aligned," 1>&2
-#		echo "" 1>&2
-#		echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2
-#		echo "" 1>&2
-#		echo " --localpair :      All pairwise local alignment information is included"  1>&2
-#		echo "                    to the objective function, default: off"  1>&2
-#		echo " --globalpair :     All pairwise global alignment information is included"  1>&2
-#		echo "                    to the objective function, default: off"  1>&2
-#		echo " --op # :           Gap opening penalty, default: $defaultgop " 1>&2
-#		echo " --ep # :           Offset (works like gap extension penalty), default: $defaultaof " 1>&2
-#		echo " --bl #, --jtt # :  Scoring matrix, default: BLOSUM62" 1>&2
-#		echo "                    Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2
-#		echo "                    or JTT (--jtt) # PAM. " 1>&2
-#		echo " --nuc or --amino : Sequence type, default: auto" 1>&2
-#		echo " --retree # :       The number of tree building in progressive method " 1>&2
-#		echo "                    (see the paper for detail), default: $defaultcycle " 1>&2
-#		echo " --maxiterate # :   Maximum number of iterative refinement, default: $defaultiterate " 1>&2
-#		if [ $defaultfft -eq 1 ]; then
-#			echo " --fft or --nofft:  FFT is enabled or disabled, default: enabled" 1>&2
-#		else
-#			echo " --fft or --nofft:  FFT is enabled or disabled, default: disabled" 1>&2
-#		fi
-#		echo " --memsave:         Memory saving mode" 1>&2
-#		echo "                    (for long genomic sequences), default: off" 1>&2
-#		echo " --clustalout :     Output: clustal format, default: fasta" 1>&2
-#		echo " --reorder :        Outorder: aligned, default: input order" 1>&2
-#		echo " --quiet :          Do not report progress" 1>&2
-#		echo "-----------------------------------------------------------------------------" 1>&2
-		exit 1; 
-	fi
-	if [ $sw -eq 1 ]; then
-		swopt=" -A "
-	else
-		swopt=" "
-	fi
-
-	if [ $distance = "fasta" -o $partdist = "fasta" ]; then
-		if [ ! "$FASTA_4_MAFFT" ]; then
-			FASTA_4_MAFFT=`which fasta34`
-		fi
-
-		if [ ! -x "$FASTA_4_MAFFT" ]; then
-			echo ""       1>&2
-			echo "== Install FASTA ========================================================" 1>&2
-			echo "This option requires the fasta34 program (FASTA version x.xx or higher)"   1>&2
-			echo "installed in your PATH.  If you have the fasta34 program but have renamed" 1>&2
-			echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2
-			echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $distance = "lara" -o $distance = "slara" ]; then
-		if [ ! -x "$prefix/mafft_lara" ]; then
-			echo ""       1>&2
-			echo "== Install LaRA =========================================================" 1>&2
-			echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)."     1>&2
-			echo "The executable have to be renamed to 'mafft_lara' and installed into "     1>&2
-			echo "the $prefix directory. "                                                   1>&2
-			echo "A configuration file of LaRA also have to be given"                        1>&2
-			echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
-			echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-		if [ ! -s "$laraparams" ]; then
-			echo ""       1>&2
-			echo "== Configure LaRA =======================================================" 1>&2
-			echo "A configuration file of LaRA have to be given"                             1>&2
-			echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
-			echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
-	if [ ! -x "$prefix/foldalign210" ]; then
-			echo ""       1>&2
-			echo "== Install FOLDALIGN ====================================================" 1>&2
-			echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2
-			echo "The executable have to be renamed to 'foldalign210' and installed into "   1>&2
-			echo "the $prefix directory. "                                                   1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $distance = "scarna" ]; then
-		if [ ! -x "$prefix/mxscarnamod" ]; then
-			echo ""       1>&2
-			echo "== Install MXSCARNA ======================================================" 1>&2
-			echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required."          1>&2
-			echo "Please 'make' at the 'extensions' directory of the MAFFT source package,"   1>&2
-			echo "which contains the modified version of MXSCARNA."                           1>&2
-			echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html "                1>&2
-			echo "==========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $mccaskill -eq 1 ]; then
-		if [ ! -x "$prefix/mxscarnamod" ]; then
-			echo ""       1>&2
-			echo "== Install MXSCARNA ======================================================" 1>&2
-			echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required."          1>&2
-			echo "Please 'make' at the 'extensions' directory of the MAFFT source package,"   1>&2
-			echo "which contains the modified version of MXSCARNA."                           1>&2
-			echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html "                1>&2
-			echo "==========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $contrafold -eq 1 ]; then
-		if [ ! -x "$prefix/contrafold" ]; then
-			echo ""       1>&2
-			echo "== Install CONTRAfold ===================================================" 1>&2
-			echo "This option requires CONTRAfold"                                           1>&2
-			echo "(Do et al. http://contra.stanford.edu/contrafold/)."                       1>&2
-			echo "The executable 'contrafold' have to be installed into "                    1>&2
-			echo "the $prefix directory. "                                                   1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-
-#old
-#	if [ $treeout -eq 1 ]; then
-#		parttreeoutopt="-t"
-#		if [ $cycle -eq 0 ]; then
-#			treeoutopt="-t -T"
-#			groupsize=1
-#			iterate=0 
-#			if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-#				distance="distonly"
-#			fi
-#		else
-#			treeoutopt="-t"
-#		fi
-#	else
-#		parttreeoutopt=" "
-#		if [ $cycle -eq 0 ]; then
-#			treeoutopt="-t -T"
-#			iterate=0 
-#			if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-#				distance="distonly"
-#			fi
-#		else
-#			treeoutopt=" "
-#		fi
-#	fi
-
-#new
-	if [ $cycle -eq 0 ]; then
-		treeoutopt="-t -T"
-		iterate=0 
-		if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-			distance="distonly"
-		fi
-		if [ $treeout -eq 1 ]; then
-			parttreeoutopt="-t"
-			groupsize=1
-		else
-			parttreeoutopt=" "
-		fi
-		if [ $distout -eq 1 ]; then
-			distoutopt="-y -T"
-		fi
-	else
-		if [ $treeout -eq 1 ]; then
-			parttreeoutopt="-t"
-			treeoutopt="-t"
-		else
-			parttreeoutopt=" "
-			treeoutopt=" "
-		fi
-		if [ $distout -eq 1 ]; then
-			distoutopt="-y"
-		fi
-	fi
-#
-
-	formatcheck=`grep -c '^[[:blank:]]\+>' $TMPFILE/infile | head -1 `
-	if [ $formatcheck -gt 0 ]; then
-		echo "The first character of a description line must be " 1>&2
-		echo "the greater-than (>) symbol, not a blank."           1>&2
-		echo "Please check the format around the following line(s):"  1>&2
-		grep -n '^[[:blank:]]\+>' $TMPFILE/infile  1>&2
-		exit 1
-	fi
-
-	nseq=`grep -c '^[>|=]' $TMPFILE/infile | head -1 ` 
-	if [ $nseq -eq 2 ]; then
-		cycle=1
-	fi
-	if [ $cycle -gt 3 ]; then
-		cycle=3
-	fi
-
-	if [ $nseq -gt 1000 -a $iterate -gt 1 ]; then
-		echo "Too many sequences to perform iterative refinement!" 1>&2
-		echo "Please use a progressive method." 1>&2
-		exit 1
-	fi
-
-
-	if [ $distance = "sixtuples" -a \( $seed = "x" -a $seedtable = "x" \) ]; then
-		localparam=" "
-	elif [ $distance = "sixtuples" -a \( $seed != "x" -o $seedtable != "x" \) ]; then
-		if [ $cycle -lt 2 ]; then
-			cycle=2                # nazeda
-		fi
-		localparam="-l "$weighti
-	elif [ $distance = "parttree" ]; then
-		localparam=" "
-		if [ $groupsize -gt -1 ]; then
-			cycle=1
-		fi
-	else
-		localparam=" -l "$weighti
-		if [ $cycle -gt 1 ]; then  # 09/01/08
-			cycle=1
-		fi
-	fi
-
-	if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-		aof="0.000"
-	fi
-
-	if [ "$memopt" = " -M -B " -a "$distance" != "sixtuples" ]; then
-		echo "Impossible" 1>&2
-		exit 1
-	fi
-#exit
-
-	if [ $distance = "parttree" ]; then
-		if [ $seed != "x" -o $seedtable != "x" ]; then
-			echo "Impossible" 1>&2
-			exit 1
-		fi
-		if [ $iterate -gt 1 ]; then
-			echo "Impossible" 1>&2
-			exit 1
-		fi
-		if [ $outorder = "aligned" ]; then
-			outorder="input"
-		fi
-		outorder="input"   # partorder ga kiku
-		if [ $partdist = "localalign" ]; then
-			splitopt=" -L "    # -L -l -> fast 
-		elif [ $partdist = "fasta" ]; then
-			splitopt=" -S "
-		else
-			splitopt="  "
-		fi
-	fi
-
-
-#	if [ $nseq -gt 5000 ]; then
-#		fft=0
-#	fi
-	if [ $forcefft -eq 1 ]; then
-		param_fft=" -G "
-		fft=1
-	elif [ $fft -eq 1 ]; then
-		param_fft=" -F "
-	else
-		param_fft=" "
-	fi
-
-	if [ $seed != "x" -a $seedtable != "x" ]; then
-			echo 'Use either one of seedtable and seed.  Not both.' 1>&2
-			exit 1
-	fi
-
-	if [ $treein -eq 1 ]; then
-#		if [ $iterate -gt 0 ]; then
-#			echo 'Not supported yet.' 1>&2
-#			exit 1
-#		fi
-		cycle=1
-	fi
-
-	if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
-		if [ $distance = "sixtuples" ]; then
-			echo 'Not supported.' 1>&2
-			echo 'Please add --globalpair, --localpair, --scarnapair,' 1>&2
-			echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
-			exit 1
-		fi
-	fi
-
-	if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
-		if [ $distance = "scarna" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
-			strategy="X-I"
-		elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
-			strategy="Q-I"
-		fi
-	elif [ $distance = "fasta" -a $sw -eq 0 ]; then
-		strategy="F-I"
-	elif [ $distance = "fasta" -a $sw -eq 1 ]; then
-		strategy="H-I"
-	elif [ $distance = "blast" ]; then
-		strategy="B-I"
-	elif [ $distance = "global" -o $distance = "distonly" ]; then
-		strategy="G-I"
-	elif [ $distance = "local" ]; then
-		strategy="L-I"
-	elif [ $distance = "localgenaf" ]; then
-		strategy="E-I"
-	elif [ $distance = "globalgenaf" ]; then
-		strategy="K-I"
-	elif [ $fft -eq 1 ]; then
-		strategy="FFT-"
-	else
-		strategy="NW-"
-	fi
-	strategy=$strategy"NS-"
-	if [ $iterate -gt 0 ]; then
-		strategy=$strategy"i"
-	elif [ $distance = "parttree" ]; then
-		if [ $partdist = "fasta" ]; then
-			strategy=$strategy"FastaPartTree-"$cycle
-		elif [ $partdist = "localalign" ]; then
-			strategy=$strategy"DPPartTree-"$cycle
-		else
-			strategy=$strategy"PartTree-"$cycle
-		fi
-	else
-		strategy=$strategy$cycle
-	fi
-
-	explanation='?'
-	performance='Not tested.'
-	if [ $strategy = "F-INS-i" ]; then
-		explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
-		performance='Most accurate, but very slow'
-	elif [ $strategy = "L-INS-i" ]; then
-		explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
-		performance='Probably most accurate, very slow'
-	elif [ $strategy = "E-INS-i" ]; then
-		explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)'
-		performance='Suitable for sequences with long unalignable regions, very slow'
-	elif [ $strategy = "G-INS-i" ]; then
-		explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information'
-		performance='Suitable for sequences of similar lengths, very slow'
-	elif [ $strategy = "X-INS-i" ]; then
-		explanation='RNA secondary structure information is taken into account.'
-		performance='For short RNA sequences only, extremely slow'
-	elif [ $strategy = "F-INS-1" ]; then
-		explanation='Progressive method incorporating LOCAL pairwise alignment information'
-	elif [ $strategy = "L-INS-1" ]; then
-		explanation='Progressive method incorporating LOCAL pairwise alignment information'
-	elif [ $strategy = "G-INS-1" ]; then
-		explanation='Progressive method incorporating GLOBAL pairwise alignment information'
-	elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then
-		explanation='Iterative refinement method (max. '$iterate' iterations)'
-		if [ $iterate -gt 2 ]; then
-			performance='Accurate but slow'
-		else
-			performance='Standard'
-		fi
-	elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then
-		explanation='Progressive method (guide trees were built '$cycle' times.)'
-		performance='Fast but rough'
-	elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then
-		explanation='Progressive method (rough guide tree was used.)'
-		performance='Very fast but very rough'
-	fi
-
-	if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
-		outputopt=" -c $strategy -r order  "
-	elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
-		outputopt=" -c $strategy  "
-	elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
-		outputopt=" -f -r order "
-	else
-		outputopt="null"
-	fi
-	
-	(
-		cd $TMPFILE;
-		if [ $quiet -gt 0 ]; then
-			if [ $seed != "x" ]; then
-				mv infile infile2
-				cat /dev/null > infile
-				cat /dev/null > hat3.seed
-				seedoffset=0
-#				echo "seednseq="$seednseq
-#				echo "seedoffset="$seedoffset
-				set $seednseq > /dev/null
-#				echo $#
-				while [ $# -gt 1 ]
-				do
-					shift
-#					echo "num="$#
-					"$prefix/multi2hat3s" -t $nseq  -o $seedoffset -i seed$# >> infile 2>/dev/null || exit 1
-					cat hat3 >> hat3.seed
-#					echo "$1"
-					seedoffset=`expr $seedoffset + $1`
-#					echo "$1"
-#					echo "seedoffset="$seedoffset
-				done;
-#				echo "seedoffset="$seedoffset
-				cat infile2 >> infile
-			elif [ $seedtable != "x" ]; then
-				cat _seedtablefile > hat3.seed
-			else
-				cat /dev/null > hat3.seed
-			fi
-#			cat hat3.seed
-			if [ $mccaskill -eq 1 ]; then
-				"$prefix/mccaskillwrap" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
-			elif [ $contrafold -eq 1 ]; then
-				"$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
-			fi
-			if [ $distance = "fasta" ]; then
-				"$prefix/dndfast7" $swopt < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "blast" ]; then
-				"$prefix/dndblast" < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "foldalignlocal" ]; then
-				"$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "foldalignglobal" ]; then
-				"$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "slara" ]; then
-				"$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "lara" ]; then
-				"$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "scarna" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "global" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -F < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "local" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $lexp -f $lgop  -h $laof -L < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "globalgenaf" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null 2>&1    || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "localgenaf" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null  2>&1      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "distonly" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null  2>&1      || exit 1
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "parttree" ]; then
-				"$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre 2>/dev/null || exit 1
-				mv hat3.seed hat3
-			else
-				"$prefix/disttbfast" $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $algopt $treealg < infile   > pre 2>/dev/null || exit 1
-				mv hat3.seed hat3
-			fi
-			while [ $cycle -gt 1 ]
-			do
-				if [ $distance = "parttree" ]; then
-					mv pre infile
-					"$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre 2>/dev/null || exit 1
-				else
-					"$prefix/tbfast" $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model  -f "-"$gop  -h "-"$aof $param_fft  $localparam $algopt -J $treealg < pre > /dev/null 2>&1 || exit 1
-				fi
-				cycle=`expr $cycle - 1`
-			done
-			if [ $iterate -gt 0 ]; then
-				if [ $distance = "sixtuples" ]; then
-				    "$prefix/dndpre"       < pre     > /dev/null 2>&1 || exit 1
-				fi
-				"$prefix/dvtditr" $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof  -I $iterate $weightopt $treeinopt $algoptit $treealg < pre     > /dev/null 2>&1 || exit 1
-			fi
-		else
-			if [ $seed != "x" ]; then
-				mv infile infile2
-				cat /dev/null > infile
-				cat /dev/null > hat3.seed
-				seedoffset=0
-#				echo "seednseq="$seednseq
-#				echo "seedoffset="$seedoffset
-				set $seednseq > /dev/null
-#				echo $#
-				while [ $# -gt 1 ]
-				do
-					shift
-#					echo "num="$#
-					"$prefix/multi2hat3s" -t $nseq  -o $seedoffset -i seed$# >> infile  || exit 1
-					cat hat3 >> hat3.seed
-#					echo "$1"
-					seedoffset=`expr $seedoffset + $1`
-#					echo "$1"
-#					echo "seedoffset="$seedoffset
-				done;
-#				echo "seedoffset="$seedoffset
-				cat infile2 >> infile
-			elif [ $seedtable != "x" ]; then
-				cat _seedtablefile > hat3.seed
-			else
-				cat /dev/null > hat3.seed
-			fi
-#			cat hat3.seed
-			if [ $mccaskill -eq 1 ]; then
-				"$prefix/mccaskillwrap" -d "$prefix" -i infile > hat4  || exit 1
-			elif [ $contrafold -eq 1 ]; then
-				"$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4  || exit 1
-			fi
-			if [ $distance = "fasta" ]; then
-				"$prefix/dndfast7" $swopt < infile > /dev/null     || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
-			elif [ $distance = "blast" ]; then
-				"$prefix/dndblast" < infile > /dev/null     || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
-			elif [ $distance = "foldalignlocal" ]; then
-				"$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "foldalignglobal" ]; then
-				"$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $pgexp -f $pggop  -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "slara" ]; then
-				"$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "lara" ]; then
-				"$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "scarna" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null   || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
-			elif [ $distance = "global" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof   -F  < infile > /dev/null     || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
-			elif [ $distance = "local" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $lexp -f $lgop  -h $laof -L  < infile > /dev/null     || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
-			elif [ $distance = "globalgenaf" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null     || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
-			elif [ $distance = "localgenaf" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N  < infile > /dev/null     || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
-			elif [ $distance = "distonly" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null            || exit 1
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
-			elif [ $distance = "parttree" ]; then
-				"$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre || exit 1
-				mv hat3.seed hat3
-			else
-				"$prefix/disttbfast" $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft  $algopt $treealg < infile   > pre || exit 1
-				mv hat3.seed hat3
-			fi
-
-			while [ $cycle -gt 1 ]
-			do
-				if [ $distance = "parttree" ]; then
-					mv pre infile
-					"$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile  > pre || exit 1
-				else
-					"$prefix/tbfast" $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model  -f "-"$gop  -h "-"$aof $param_fft $localparam $algopt -J $treealg < pre > /dev/null || exit 1
-				fi
-				cycle=`expr $cycle - 1`
-			done
-			if [ $iterate -gt 0 ]; then
-				if [ $distance = "sixtuples" ]; then
-			    	"$prefix/dndpre"       < pre     > /dev/null 2>&1 || exit 1
-				fi
-				"$prefix/dvtditr" $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof -I $iterate $weightopt $treeinopt $algoptit $treealg < pre     > /dev/null || exit 1
-			fi
-		fi
-
-
-
-		if [ $coreout -eq 1 ]; then
-			"$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2
-			mv pre2 pre
-		fi
-		if [ "$outputopt" = "null" ]; then
-			cat < pre || exit 1
-		else
-			"$prefix/f2cl" $outputopt < pre || exit 1
-		fi
-	)
-
-	if [ $treeout -eq 1 ]; then
-		cp $TMPFILE/infile.tree "$infilename.tree"
-	fi
-
-	if [ $distout -eq 1 ]; then
-		cp $TMPFILE/hat2 "$infilename.hat2"
-	fi
-
-	if [ $quiet -eq 0 ]; then
-		echo '' 1>&2
-		if [ $mccaskill -eq 1 ]; then
-			echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>&2
-			echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>&2
-			echo "incorporated in the iterative alignment process (4)." 1>&2
-			echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>&2
-			echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>&2
-			echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>&2
-			echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
-			echo "" 1>&2
-		elif [ $contrafold -eq 1 ]; then
-			echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>&2
-			echo "and then incorporated in the iterative alignment process (4)." 1>&2
-			echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>&2
-			echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
-			echo "" 1>&2
-		fi
-		if [ $distance = "fasta" -o $partdist = "fasta" ]; then
-			echo "Pairwise alignments were computed by FASTA" 1>&2
-			echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>&2
-		fi
-		if [ $distance = "blast" ]; then
-			echo "Pairwise alignments were computed by BLAST" 1>&2
-			echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>&2
-		fi
-		if [ $distance = "scarna" ]; then
-			echo "Pairwise alignments were computed by MXSCARNA" 1>&2
-			echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>&2
-		fi
-		if [ $distance = "lara" -o $distance = "slara" ]; then
-			echo "Pairwise alignments were computed by LaRA" 1>&2
-			echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>&2
-		fi
-		if [ $distance = "foldalignlocal" ]; then
-			echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>&2
-			echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
-		fi
-		if [ $distance = "foldalignglobal" ]; then
-			echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>&2
-			echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
-		fi
-		printf "\n" 1>&2
-		echo 'Strategy:' 1>&2
-		printf ' '$strategy 1>&2
-		echo ' ('$performance')' 1>&2
-		echo ' '$explanation 1>&2
-		echo '' 1>&2
-		echo "If unsure which option to use, try 'mafft --auto input > output'." 1>&2
-#		echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>&2
-		echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>&2
-		echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>&2
-		echo '' 1>&2
-	fi
-	exit 0;
-fi
-
-prog="awk"
-
-tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
-if [ -x "$tmpawk" ]; then
-	prog="$tmpawk"
-fi
-
-tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
-if [ -x "$tmpawk" ]; then
-	prog="$tmpawk"
-fi
-
-echo "prog="$prog 1>&2
-
-umask 077
-export defaultaof
-export defaultgop
-export defaultfft
-export defaultcycle
-export defaultiterate
-(
-$prog '
-BEGIN {
-	prefix = ENVIRON["prefix"];
-	version = ENVIRON["version"];
-	myself = ENVIRON["myself"];
-	defaultgop = ENVIRON["defaultgop"]
-	defaultaof = ENVIRON["defaultaof"]
-	defaultfft = ENVIRON["defaultfft"]
-	defaultcycle = ENVIRON["defaultcycle"]
-	defaultiterate = ENVIRON["defaultiterate"]
-	while( 1 )
-	{
-		options = ""
-		printf( "\n" ) > "/dev/tty";
-		printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
-		printf( "\n" )                                                                           > "/dev/tty";
-		printf( "   MAFFT %s\n", version )                                                       > "/dev/tty";
-		printf( "\n" )                                                                           > "/dev/tty";
-		printf( "        Copyright (c) 2009 Kazutaka Katoh\n" )                                  > "/dev/tty";
-		printf( "        NAR 30:3059-3066, NAR 33:511-518\n" )                                   > "/dev/tty";
-		printf( "        http://align.bmr.kyushu-u.ac.jp/mafft/software/\n" )       > "/dev/tty";
-		printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
-		printf( "\n" ) > "/dev/tty";
-	
-		while( 1 )
-		{
-			printf( "\n" ) > "/dev/tty";
-			printf( "Input file? (fasta format)\n@ " ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" )
-			if( res == 0 || NF == 0 )
-				continue;
-			infile0 = sprintf( "%s", $1 );
-			infile = sprintf( "%s", $1 );
-	
-			res = getline < infile;
-			close( infile );
-			if( res == -1 )
-				printf( "%s: No such file.\n\n", infile ) > "/dev/tty";
-			else if( res == 0 )
-				printf( "%s: Empty.\n", infile ) > "/dev/tty";
-			else
-			{
-				printf( "OK. infile = %s\n\n", infile ) > "/dev/tty";
-				break;
-			}
-		}
-		nseq = 0;
-	
-		while( 1 )
-		{
-			printf( "\n" ) > "/dev/tty";
-			printf( "Output file?\n" ) > "/dev/tty";
-			printf( "@ " ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 || NF == 0 )
-				continue;
-			else
-			{
-				outfile = sprintf( "%s", $1 );
-				printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
-				break;
-			}
-		}
-	
-	
-		while( 1 )
-		{
-			retree = defaultcycle
-			printf( "\n" ) > "/dev/tty";
-			printf( "Number of tree-rebuilding?\n" ) > "/dev/tty";
-			printf( "@ [%d] ", retree ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 0 )
-				;
-			else
-				retree = 0 + $1;
-			if( retree < 1 || 10 < retree )
-				;
-			else
-			{
-				printf( "OK. %d\n\n", retree ) > "/dev/tty";
-				break;
-			}
-		}
-	
-		while( 1 )
-		{
-			niterate = defaultiterate;
-			printf( "\n" ) > "/dev/tty";
-			printf( "Maximum number of iterations?\n" ) > "/dev/tty";
-			printf( "@ [%d] ", niterate ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 0 )
-				;
-			else
-				niterate = 0 + $1;
-			if( niterate < 0 || 1000 < niterate )
-				;
-			else
-			{
-				printf( "OK. %d\n\n", niterate ) > "/dev/tty";
-				break;
-			}
-		}
-
-		while( 1 )
-		{
-			fft = defaultfft;
-			printf( "\n" ) > "/dev/tty";
-			printf( "Use fft?\n" ) > "/dev/tty";
-			printf( "@ [%s] ", fft?"Yes":"No" ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 0 )
-			{
-				break;
-			}
-			else if( NF == 0 || $0 ~ /^[Yy]/ )
-			{
-				fft = 1;
-				break;
-			}
-			else if( NF == 0 || $0 ~ /^[Nn]/ )
-			{
-				fft = 0;
-				break;
-			}
-		}
-		if( fft )
-		{
-				printf( "OK. FFT is enabled.\n\n" ) > "/dev/tty";
-				fftparam = " ";
-		}
-		else
-		{
-				printf( "OK. FFT is disabled.\n\n" ) > "/dev/tty";
-				fftparam = " --nofft ";
-		}
-
-		while( 1 )
-		{
-			scoringmatrix = 3;
-			printf( "\n" ) > "/dev/tty";
-			printf( "Scoring matrix? (ignored when DNA sequence is input.)\n" ) > "/dev/tty";
-			printf( " 1. BLOSUM 30\n" ) > "/dev/tty";
-			printf( " 2. BLOSUM 45\n" ) > "/dev/tty";
-			printf( " 3. BLOSUM 62\n" ) > "/dev/tty";
-			printf( " 4. BLOSUM 80\n" ) > "/dev/tty";
-			printf( " 5. JTT 200\n" ) > "/dev/tty";
-			printf( " 6. JTT 100\n" ) > "/dev/tty";
-			printf( "@ [%d] ", scoringmatrix ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 0 )
-				;
-			else
-				scoringmatrix = 0 + $1;
-			if( scoringmatrix < 1 || 6 < scoringmatrix )
-				;
-			else
-			{
-				break;
-			}
-		}
-		if( scoringmatrix == 1 )
-			scoringparam = " --bl 30 ";
-		else if( scoringmatrix == 2 )
-			scoringparam = " --bl 45 ";
-		else if( scoringmatrix == 3 )
-			scoringparam = " --bl 62 ";
-		else if( scoringmatrix == 4 )
-			scoringparam = " --bl 80 ";
-		else if( scoringmatrix == 5 )
-			scoringparam = " --jtt 200 ";
-		else if( scoringmatrix == 6 )
-			scoringparam = " --jtt 100 ";
-		printf( "OK. %s\n\n",scoringparam ) > "/dev/tty";
-	
-		while( 1 )
-		{
-			penalty = 0.0 + defaultgop;
-			offset = 0.0 + defaultaof;
-			printf( "\n" ) > "/dev/tty";
-			printf( "Parameters (gap opening penalty, offset)?\n", penalty, offset ) > "/dev/tty";
-			printf( "@ [%5.3f, %5.3f] ", penalty, offset ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 2 )
-			{
-				penalty = 0.0 + $1;
-				offset = 0.0 + $2;
-			}
-			else if( NF == 0 )
-				;
-			else
-				continue;
-			if( penalty < 0.0 || 10.0 < penalty )
-				;
-			else if( offset < 0.0 || 10.0 < offset )
-				;
-			else
-			{
-				printf( "OK. %5.3f %5.3f\n\n", penalty, offset ) > "/dev/tty";
-				break;
-			}
-		}
-	
-		command = sprintf( "\"%s\" %s --retree %d --maxiterate %d %s --op %f --ep %f %s > %s", myself, fftparam, retree, niterate, scoringparam, penalty, offset, infile, outfile );
-		gsub( /\\/, "/", command );
-
-
-		printf( "%s\n\n", command ) > "/dev/tty";
-	
-	
-		while( 1 )
-		{
-			go = 0;
-			printf( "\n" ) > "/dev/tty";
-			printf( "OK?\n" ) > "/dev/tty";
-			printf( "@ [Y] " ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 0 || $0 ~ /^[Yy]/ )
-			{
-				go=1;
-				break;
-			}
-			else
-				break;
-		}
-		if( go ) break;
-		printf( "\n" ) > "/dev/tty";
-		printf( "\n" ) > "/dev/tty";
-	}
-	system( command );
-	printf( "Press Enter to exit." ) > "/dev/tty";
-	res = getline < "/dev/tty";
-}
-'
-)
-exit 0;