diff --git "a/mafft/mafftdir/bin/mafft" "b/mafft/mafftdir/bin/mafft"
new file mode 100644--- /dev/null
+++ "b/mafft/mafftdir/bin/mafft"
@@ -0,0 +1,3069 @@
+#! /bin/bash 
+er=0;
+myself=`dirname "$0"`/`basename "$0"`; export myself
+version="v7.526 (2024/Apr/26)"; export version
+LANG=C; export LANG
+os=`uname`
+progname=`basename "$0"`
+windows="no"
+if [ `echo $os | grep -i cygwin` ]; then
+	os="cygwin"
+	windows="yes"
+elif [ `echo $os | grep -i msys` ]; then
+	os="msys"
+	windows="yes"
+elif [ `echo $os | grep -i mingw` ]; then
+	os="mingw"
+	windows="yes"
+elif [ `echo $os | grep -i darwin` ]; then
+	os="darwin"
+elif [ `echo $os | grep -i sunos` ]; then
+	os="sunos"
+elif [ `echo $os | grep -i linux` ]; then
+	os="linux"
+else
+	os="unix"
+fi
+#export os # iranai
+if [ "$windows" = "yes" ]; then
+	echo "" 1>&2
+	echo "It may take a while before the calculation starts" 1>&2
+	echo "if being scanned by anti-virus software." 1>&2
+	echo "Also consider using a faster version for Windows 10:" 1>&2
+	echo "https://mafft.cbrc.jp/alignment/software/wsl.html" 1>&2
+fi
+
+if [ "$MAFFT_BINARIES" ]; then
+	prefix="$MAFFT_BINARIES"
+else
+	prefix=/usr/libexec/mafft
+fi
+export prefix # iranai
+
+if [ $# -gt 0 ]; then
+	if [ "$1" = "--man" ]; then 
+		man "$prefix/mafft.1"
+		exit 0;
+	fi
+fi
+
+if [ -x "$prefix/version" ]; then
+#		versionbin=`"$prefix/version" | awk '{print $1}'` # for cygwin
+		versionbin=`"$prefix/version"` # for cygwin 2.7
+	else
+		versionbin="0.000"
+fi
+
+if ! expr "$version" : v"$versionbin" > /dev/null ; then
+	echo "" 1>&2
+	echo "v$versionbin != $version" 1>&2
+	echo "" 1>&2
+	echo "There is a problem in the configuration of your shell." 1>&2
+	echo "Check the MAFFT_BINARIES environmental variable by" 1>&2
+	echo "$ echo \$MAFFT_BINARIES" 1>&2
+	echo "" 1>&2
+	echo "This variable must be *unset*, unless you have installed MAFFT" 1>&2
+	echo "with a special configuration.  To unset this variable, type" 1>&2
+	echo "$ unset MAFFT_BINARIES" 1>&2
+	echo "or" 1>&2
+	echo "% unsetenv MAFFT_BINARIES" 1>&2
+	echo "Then retry" 1>&2
+	echo "$ mafft input > output" 1>&2
+	echo "" 1>&2
+	echo "To keep this change permanently, edit setting files" 1>&2
+	echo "(.bash_profile, .profile, .cshrc, etc) in your home directory" 1>&2
+	echo "to delete the MAFFT_BINARIES line." 1>&2
+	echo "On MacOSX, also edit or remove the .MacOSX/environment.plist file" 1>&2
+	echo "and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7)." 1>&2
+	echo "" 1>&2
+	echo "Please send a problem report to katoh@ifrec.osaka-u.ac.jp," 1>&2
+	echo "if this problem remains." 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="ktuples"
+#defaultdistance="local"
+defaultweighti="2.7"
+defaultweightr="0.0"
+defaultweightm="1.0"
+defaultdafs=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
+	defaultdafs=0
+	defaultalgopt=" -A "
+	defaultalgoptit=" -AB " ## chui
+	defaultaof="0.0"
+	defaultsbstmodel=" -b 62 "
+	defaultkappa=" "
+	defaultfmodel="    "  # 2013/06/18
+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
+	defaultdafs=0
+	defaultalgopt=" -A "
+	defaultalgoptit=" -AB " ## chui
+	defaultaof="0.0"
+	defaultsbstmodel=" -b 62 "
+	defaultkappa=" "
+	defaultfmodel="    "  # 2013/06/18
+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="ktuples"
+elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
+	defaultfft=1
+	defaultcycle=2
+	defaultiterate=2
+	defaultdistance="ktuples"
+elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
+	defaultfft=0
+	defaultcycle=2
+	defaultdistance="ktuples"
+elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
+	defaultfft=0
+	defaultcycle=2
+	defaultiterate=2
+	defaultdistance="ktuples"
+fi
+outputfile=""
+namelength=-1
+linelength=60 # Will change to -1 in the future
+anysymbol=0
+parallelizationstrategy="BAATARI2"
+kappa=$defaultkappa
+sbstmodel=$defaultsbstmodel
+fmodel=$defaultfmodel
+nmodel=" "
+gexp=0
+gop=$defaultgop
+gopdist=$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=$defaultweightm
+rnaalifold=0
+dafs=$defaultdafs
+mccaskill=$defaultmccaskill
+contrafold=$defaultcontrafold
+progressfile="/dev/stderr"
+anchorfile="/dev/null"
+anchoropt=""
+#maxanchorseparation=1000
+#maxanchorseparation=-1 # 2023/Jan/11
+terminalmargin=100 # 2024/Mar
+debug=0
+sw=0
+algopt=$defaultalgopt
+algoptit=$defaultalgoptit
+#algspecified=0
+pairspecified=0
+scorecalcopt=" "
+coreout=0
+corethr="0.5"
+corewin="100"
+coreext=" "
+outputformat="pir"
+f2clext="-N"
+outorder="input"
+seed="x"
+seedtable="x"
+auto=0
+groupsize=-1
+partsize=50
+partdist="ktuples"
+partorderopt=" -x "
+treeout=0
+nodeout=0
+distout=0
+distformat="hat2"
+treein=0
+topin=0
+treeinopt="  "
+seedfiles="/dev/null"
+seedtablefile="/dev/null"
+pdblist="/dev/null"
+ownlist="/dev/null"
+strdir="$PWD"
+scorematrix="/dev/null"
+textmatrix="/dev/null"
+treeinfile="/dev/null"
+codonposfile="/dev/null"
+codonscorefile="/dev/null"
+rnascoremtx=" "
+laraparams="/dev/null"
+foldalignopt=" "
+treealg=" -X 0.1 "
+sueff="1.0"
+maxambiguous="1.0"
+dofilter=0
+scoreoutarg=" "
+numthreads=0
+numthreadsit=-1
+numthreadstb=-1
+randomseed=0
+addfile="/dev/null"
+addarg0=" "
+addarg=" "
+addsinglearg=" "
+add2ndhalfarg=" "
+mapoutfile="/dev/null"
+fragment=0
+legacygapopt=" "
+mergetable="/dev/null"
+mergearg=" "
+seedoffset=0
+outnum=" "
+last_e=5000
+last_m=3
+last_subopt=" "
+last_once=" "
+adjustdirection=0
+tuplesize=6
+termgapopt=" -O "
+#termgapopt=" " # gap/gap ga kakenai node
+similarityoffset="0.0"
+unalignlevel="0.0"
+unalignspecified=0
+spfactor="100.0"
+shiftpenaltyspecified=0
+opdistspecified=0
+allowshift=0
+enrich=0        # ato de kezuru
+enrichseq=0     # ato de kezuru
+enrichstr=0     # ato de kezuru
+seektarget=""   # ato de kezuru
+dashserver="https://sysimm.org/dash/REST1.0/"
+newdash=0
+newdash_originalsequenceonly=0
+exclude_ho=0
+fixthreshold="0.0"
+bunkatsuopt=" "
+npickup=0
+minimumweight="0.00001" # 2016/Mar
+usenaivepairscore=" "
+oldgenafparam=0
+sprigorous=0
+treeext="none"
+initialramusage="20GB"
+focusarg=" "
+lhlimit=" "
+mpiscript="/dev/null"
+if [ $# -gt 0 ]; then
+	if [ "$1" = "--version" ]; then
+		echo "$version" 1>&2
+		exit 0;
+	elif [ "$1" = "--help" -o "$1" = "--info" ]; then 
+		shift
+		er=1;
+	fi
+	while [ $# -gt 1 ];
+	do
+		if [ "$1" = "--auto" ]; then 
+			auto=1
+		elif [ "$1" = "--anysymbol" ]; then 
+			anysymbol=1
+		elif [ "$1" = "--preservecase" ]; then 
+			anysymbol=1
+		elif [ "$1" = "--clustalout" ]; then 
+			outputformat="clustal"
+		elif [ "$1" = "--phylipout" ]; then 
+			outputformat="phylip"
+		elif [ "$1" = "--reorder" ]; then 
+			outorder="aligned"
+			partorderopt=" "
+		elif [ "$1" = "--inputorder" ]; then 
+			outorder="input"
+			partorderopt=" -x "
+		elif [ "$1" = "--unweight" ]; then 
+			weightopt=" -u "
+		elif [ "$1" = "--termgappenalty" ]; then 
+			termgapopt=" "
+		elif [ "$1" = "--alga" ]; then 
+			algopt=" "
+			algoptit=" "
+#			algspecified=1
+		elif [ "$1" = "--algq" ]; then 
+			algopt=" -Q "
+			algoptit=" "
+			echo "" 1>&2
+			echo "--algq is no longer supported!" 1>&2
+			echo "" 1>&2
+			exit 1;
+#			algspecified=1
+		elif [ "$1" = "--linelength" ]; then 
+			shift   
+			linelength=`expr "$1" - 0`
+			if [ $linelength -eq 0 ]; then
+				echo "Line length = 0 ?" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--namelength" ]; then 
+			shift   
+			namelength=`expr "$1" - 0`
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify the length of name in clustal format output!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--groupsize" ]; then 
+			shift   
+			groupsize=`expr "$1" - 0`
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify groupsize!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--partsize" ]; then 
+			shift   
+			partsize=`expr "$1" - 0`
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify partsize!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--parttree" ]; then 
+			distance="parttree"
+			partdist="ktuples"
+		elif [ "$1" = "--dpparttree" ]; then 
+			distance="parttree"
+			partdist="localalign"
+		elif [ "$1" = "--fastaparttree" ]; then 
+			distance="parttree"
+			partdist="fasta"
+		elif [ "$1" = "--treeout" ]; then 
+			treeout=1
+		elif [ "$1" = "--nodeout" ]; then 
+			nodeout=1
+			treeout=1
+		elif [ "$1" = "--distout" ]; then 
+			distout=1
+			distformat="hat2"
+		elif [ "$1" = "--distoutclustalo" ]; then 
+			distout=1
+			distformat="clodist"
+		elif [ "$1" = "--fastswpair" ]; then
+			distance="fasta"
+			pairspecified=1
+			sw=1
+		elif [ "$1" = "--fastapair" ]; then
+			distance="fasta"
+			pairspecified=1
+			sw=0
+		elif [ "$1" = "--averagelinkage" ]; then
+			treealg=" -X 1.0 "
+			sueff="1.0"
+		elif [ "$1" = "--minimumlinkage" ]; then
+			treealg=" -X 0.0 "
+			sueff="0.0"
+		elif [ "$1" = "--mixedlinkage" ]; then
+			shift   
+			sueff="$1"
+			treealg=" -X $1"
+		elif [ "$1" = "--maxambiguous" ]; then
+			shift   
+			maxambiguous="$1"
+			dofilter=1
+		elif [ "$1" = "--codonpos" ]; then
+			shift   
+			codonposfile="$1"
+			if [ ! -e "$codonposfile" ]; then
+				echo "Cannot open $codonposfile" 1>&2
+				echo "" 1>&2
+				exit
+			fi
+			codonposopt=" -R "
+		elif [ "$1" = "--codonscore" ]; then
+			shift   
+			codonscorefile="$1"
+			if [ ! -e "$codonscorefile" ]; then
+				echo "Cannot open $codonscorefile" 1>&2
+				echo "" 1>&2
+				exit
+			fi
+			codonscoreopt=" -S "
+		elif [ "$1" = "--noscore" ]; then
+			scorecalcopt=" -Z "
+		elif [ "$1" = "--6mermultipair" ]; then
+			distance="ktuplesmulti"
+			tuplesize=6
+			pairspecified=1
+		elif [ "$1" = "--10mermultipair" ]; then
+			distance="ktuplesmulti"
+			tuplesize=10
+			pairspecified=1
+		elif [ "$1" = "--6merpair" ]; then
+			distance="ktuples"
+			tuplesize=6
+			pairspecified=1
+		elif [ "$1" = "--10merpair" ]; then
+			distance="ktuples"
+			tuplesize=10
+			pairspecified=1
+		elif [ "$1" = "--blastpair" ]; then
+			distance="blast"
+			pairspecified=1
+		elif [ "$1" = "--lastmultipair" ]; then
+			distance="lastmulti"
+			pairspecified=1
+		elif [ "$1" = "--globalpair" ]; then
+			distance="global"
+			pairspecified=1
+		elif [ "$1" = "--shortlongpair" ]; then
+			distance="local"
+			usenaivepairscore="-Z"
+			laof=0.0  # addfull no tokini tsukawareru.
+			lexp=0.0  # addfull no tokini tsukawareru.
+			pgaof=0.0 # local nara iranai
+			pgexp=0.0 # local nara iranai
+			pairspecified=1
+		elif [ "$1" = "--longshortpair" ]; then
+			distance="local"
+			usenaivepairscore="-Z"
+			laof=0.0  # addfull no tokini tsukawareru.
+			lexp=0.0  # addfull no tokini tsukawareru.
+			pgaof=0.0 # local nara iranai
+			pgexp=0.0 # local nara iranai
+			pairspecified=1
+		elif [ "$1" = "--localpair" ]; then
+			distance="local"
+			pairspecified=1
+		elif [ "$1" = "--lastpair" ]; then
+			distance="last"
+			pairspecified=1
+		elif [ "$1" = "--multipair" ]; then
+			distance="multi"
+			pairspecified=1
+		elif [ "$1" = "--hybridpair" ]; then
+			distance="hybrid"
+			pairspecified=1
+		elif [ "$1" = "--scarnapair" ]; then
+			distance="scarna"
+			pairspecified=1
+		elif [ "$1" = "--dafspair" ]; then
+			distance="dafs"
+			pairspecified=1
+		elif [ "$1" = "--larapair" ]; then
+			distance="lara"
+			pairspecified=1
+		elif [ "$1" = "--slarapair" ]; then
+			distance="slara"
+			pairspecified=1
+		elif [ "$1" = "--foldalignpair" ]; then
+			distance="foldalignlocal"
+			pairspecified=1
+		elif [ "$1" = "--foldalignlocalpair" ]; then
+			distance="foldalignlocal"
+			pairspecified=1
+		elif [ "$1" = "--foldalignglobalpair" ]; then
+			distance="foldalignglobal"
+			pairspecified=1
+		elif [ "$1" = "--globalgenafpair" ]; then
+			distance="globalgenaf"
+			pairspecified=1
+			echo "" 1>&2
+			echo "--globalgenaf is no longer supported!" 1>&2
+			echo "" 1>&2
+			exit 1;
+		elif [ "$1" = "--localgenafpair" ]; then
+			distance="localgenaf"
+			pairspecified=1
+		elif [ "$1" = "--genafpair" ]; then
+			distance="localgenaf"
+			pairspecified=1
+		elif [ "$1" = "--oldgenafpair" ]; then
+			distance="localgenaf"
+			pairspecified=1
+			oldgenafparam=1
+		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" # Deleted space, 2018/Dec
+		elif [ "$1" = "--amino" ]; then 
+			seqtype="-P" # Deleted space, 2018/Dec
+		elif [ "$1" = "--fft" ]; then 
+			fft=1
+			forcefft=1
+		elif [ "$1" = "--nofft" ]; then 
+			fft=0
+		elif [ "$1" = "--quiet" ]; then 
+#			if [ $os = "msys" ]; then
+#				progressfile="nul"
+#			else
+				progressfile="/dev/null"
+#			fi
+		elif [ "$1" = "--debug" ]; then 
+			debug=1
+		elif [ "$1" = "--coreext" ]; then 
+			coreext=" -c "
+		elif [ "$1" = "--core" ]; then 
+			coreout=1
+		elif [ "$1" = "--adjustdirection" ]; then 
+			adjustdirection=1
+		elif [ "$1" = "--adjustdirectionaccurately" ]; then 
+			adjustdirection=2
+		elif [ "$1" = "--oneiteration" ]; then 
+			oneiterationopt=" -r "
+		elif [ "$1" = "--progress" ]; then 
+			shift   
+			progressfile="$1"
+			if ! ( expr "$progressfile" : "\/" > /dev/null || expr "$progressfile" : "[A-Za-z]\:" > /dev/null ) ; then
+				echo "Specify a progress file name with the absolute path!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--out" ]; then 
+			shift   
+			outputfile="$1"
+		elif [ "$1" = "--terminalmargin" ]; then 
+			shift   
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "set --terminalmargin (int)." 1>&2
+				exit
+			fi
+			terminalmargin=`expr "$1" - 0` 
+		elif [ "$1" = "--anchors" ]; then 
+			shift
+			anchorfile="$1"
+			anchoropt=" -l "
+#			memopt=" -M -B "      # ato de kentou
+#			memopt=" -N "         # no memsave
+			if [ ! -e "$anchorfile" ]; then
+				echo "Cannot open $anchorfile" 1>&2
+				echo "" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--thread" ]; then 
+			shift
+			if ! expr "$1" : "[0-9\-]" > /dev/null ; then
+				echo "Specify the number of threads.  Or, use --thread -1" 1>&2
+				exit
+			fi
+			numthreads=`expr "$1" - 0` 
+		elif [ "$1" = "--threadtb" ]; then 
+			shift
+			if ! expr "$1" : "[0-9\-]" > /dev/null ; then
+				echo "Check the argument after --threadtb, the number of threads for the progressive step." 1>&2
+				exit
+			fi
+			numthreadstb=`expr "$1" - 0` 
+		elif [ "$1" = "--threadit" ]; then 
+			shift
+			if ! expr "$1" : "[0-9\-]" > /dev/null ; then
+				echo "Check the argument after --threadit, the number of threads for the iterative step." 1>&2
+				exit
+			fi
+			numthreadsit=`expr "$1" - 0` 
+		elif [ "$1" = "--last_subopt" ]; then 
+			last_subopt="-S"
+		elif [ "$1" = "--last_once" ]; then 
+			last_once="-U"
+		elif [ "$1" = "--last_m" ]; then 
+			shift
+			last_m=`expr "$1" - 0` 
+		elif [ "$1" = "--last_e" ]; then 
+			shift
+			last_e=`expr "$1" - 0` 
+		elif [ "$1" = "--randomseed" ]; then 
+			shift
+			randomseed=`expr "$1" - 0` 
+		elif [ "$1" = "--bestfirst" ]; then 
+			parallelizationstrategy="BESTFIRST"
+		elif [ "$1" = "--adhoc0" ]; then 
+			parallelizationstrategy="BAATARI0"
+		elif [ "$1" = "--adhoc1" ]; then 
+			parallelizationstrategy="BAATARI1"
+		elif [ "$1" = "--adhoc2" ]; then 
+			parallelizationstrategy="BAATARI2"
+		elif [ "$1" = "--simplehillclimbing" ]; then 
+			parallelizationstrategy="BAATARI2"
+		elif [ "$1" = "--scoreout" ]; then 
+			scoreoutarg="-S -B"
+		elif [ "$1" = "--outnum" ]; then 
+			outnum="-n"
+		elif [ "$1" = "--leavegappyregion" ]; then 
+			legacygapopt="-L"
+		elif [ "$1" = "--legacygappenalty" ]; then 
+			legacygapopt="-L"
+		elif [ "$1" = "--merge" ]; then
+			shift
+			mergetable="$1"
+			if [ ! -e "$mergetable" ]; then
+				echo "Cannot open $mergetable" 1>&2
+				echo "" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--addprofile" ]; then 
+			shift   
+			addarg0="-I"
+			addfile="$1"
+		elif [ "$1" = "--add" ]; then 
+			shift   
+			addarg0="-K -I"
+			addfile="$1"
+		elif [ "$1" = "--addfragments" ]; then 
+			shift   
+			addarg0="-K -I"
+			addfile="$1"
+			fragment=1
+		elif [ "$1" = "--addfull" ]; then 
+			shift   
+			addarg0="-K -I"
+			addfile="$1"
+			fragment=-1
+		elif [ "$1" = "--addlong" ]; then 
+			shift   
+			addarg0="-K -I"
+			addfile="$1"
+			fragment=-2
+		elif [ "$1" = "--addtotop" ]; then 
+			shift   
+			addarg0="-K -I"
+			addfile="$1"
+			fragment=-3
+		elif [ "$1" = "--addtoroot" ]; then 
+			shift   
+			addarg0="-K -I"
+			addfile="$1"
+			fragment=-4
+		elif [ "$1" = "--smoothing" ]; then 
+			add2ndhalfarg=$add2ndhalfarg" -p "
+		elif [ "$1" = "--keeplength" ]; then 
+			add2ndhalfarg=$add2ndhalfarg" -Y "
+		elif [ "$1" = "--compactmapout" ]; then 
+			add2ndhalfarg=$add2ndhalfarg" -z -Y "
+		elif [ "$1" = "--compactmapoutfile" ]; then 
+			shift
+			add2ndhalfarg=$add2ndhalfarg" -z -Y "
+			mapoutfile="$1"
+		elif [ "$1" = "--mapout" ]; then 
+			add2ndhalfarg=$add2ndhalfarg" -Z -Y "
+		elif [ "$1" = "--mapoutfile" ]; then 
+			shift
+			add2ndhalfarg=$add2ndhalfarg" -Z -Y "
+			mapoutfile="$1"
+		elif [ "$1" = "--maxiterate" ]; then 
+			shift   
+			iterate=`expr "$1" - 0` 
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify the number of iterations!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--retree" ]; then 
+			shift   
+			cycle=`expr "$1" - 0`
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify the number of tree rebuilding!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--aamatrix" ]; then 
+			shift   
+			f2clext="-N"
+			sbstmodel=" -b -1 "
+			scorematrix="$1"
+			if [ ! -e "$scorematrix" ]; then
+				echo "Cannot open $scorematrix" 1>&2
+				echo "" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--textmatrix" ]; then 
+			shift   
+			f2clext="-E"
+			seqtype="-P"
+			fft=0
+#			sbstmodel=" -b -2 -a "
+			sbstmodel=" -b -2 " # 2022/Jul, hauretsu no kawari ni scoremtx wo miru
+			scorematrix="$1"
+			if [ ! -e "$scorematrix" ]; then
+				echo "Cannot open $scorematrix" 1>&2
+				echo "" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--text" ]; then 
+			f2clext="-E"
+			seqtype="-P"
+			fft=0
+			sbstmodel=" -b -2 -a "
+		elif [ "$1" = "--treein" ]; then 
+			shift   
+			treeinopt=" -U "
+			treein=1
+			treeinfile="$1"
+			if [ ! -e "$treeinfile" ]; then
+				echo "Cannot open $treeinfile" 1>&2
+				echo "" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--pileup" ]; then 
+#			treeinopt=" -U "
+#			treein=1
+			treeext="pileup"
+		elif [ "$1" = "--randomchain" ]; then 
+#			treeinopt=" -U "
+#			treein=1
+#			pileuporshuffle="s"
+			treeext="randomchain"
+		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 [ "$1" = "--mpi" ]; then 
+			mpiscript="$prefix/mpiscript"
+		elif [ "$1" = "--large" ]; then
+			treeext="memsavetree"
+		elif [ "$1" = "--memsavetree" ]; then
+			treeext="memsavetree"
+		elif [ "$1" = "--memsavetreex" ]; then
+			treeext="memsavetreex"
+		elif [ "$1" = "--stepadd" ]; then
+			treeext="stepadd"
+		elif [ "$1" = "--youngestlinkage" ]; then
+			treeext="youngestlinkage"
+		elif [ "$1" = "--kappa" ]; then 
+			shift   
+			kappa=" -k $1 "
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify kappa value!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--fmodel" ]; then 
+			fmodel=" -a "
+		elif [ "$1" = "--nwildcard" ]; then 
+			nmodel=" -: "
+		elif [ "$1" = "--nzero" ]; then 
+			nmodel="  "
+		elif [ "$1" = "--jtt" ]; then 
+			shift   
+			f2clext="-N"
+			sbstmodel=" -j $1"
+#			if ! expr "$1" : "[0-9]" > /dev/null ; then
+#				echo "Specify pam value!" 1>&2
+#				exit
+#			fi
+		elif [ "$1" = "--kimura" ]; then 
+			shift   
+			f2clext="-N"
+			sbstmodel=" -j $1"
+#			if ! expr "$1" : "[0-9]" > /dev/null ; then
+#				echo "Specify pam value!" 1>&2
+#				exit
+#			fi
+		elif [ "$1" = "--tm" ]; then 
+			shift   
+			f2clext="-N"
+			sbstmodel=" -m $1"
+#			if ! expr "$1" : "[0-9]" > /dev/null ; then
+#				echo "Specify pam value!" 1>&2
+#				exit
+#			fi
+		elif [ "$1" = "--bl" ]; then 
+			shift   
+			f2clext="-N"
+			sbstmodel=" -b $1"
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "blosum $1?" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--weighti" ]; then
+			shift   
+			weighti="$1"
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify weighti value!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--weightr" ]; then
+			shift   
+			weightr="$1"
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify weightr value!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--weightm" ]; then
+			shift   
+			weightm="$1"
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify weightm value!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--rnaalifold" ]; then
+			rnaalifold=1
+		elif [ "$1" = "--mccaskill" ]; then
+			mccaskill=1
+			contrafold=0
+			dafs=0
+		elif [ "$1" = "--contrafold" ]; then
+			mccaskill=0
+			contrafold=1
+			dafs=0
+		elif [ "$1" = "--dafs" ]; then
+			mccaskill=0
+			contrafold=0
+			dafs=1
+		elif [ "$1" = "--ribosum" ]; then
+			rnascoremtx=" -s "
+		elif [ "$1" = "--op" ]; then 
+			shift   
+			gop="$1"
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify op!" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--opdist" ]; then 
+			shift   
+			gopdist="$1"
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify opdist!" 1>&2
+				exit
+			fi
+			opdistspecified=1
+		elif [ "$1" = "--allowshift" ]; then 
+			allowshift=1
+		elif [ "$1" = "--shiftpenalty" ]; then 
+			shift   
+			spfactor="$1"
+			if ! expr "$1" : "[0-9]" > /dev/null ; then
+				echo "Specify sf!" 1>&2
+				exit
+			fi
+			shiftpenaltyspecified=1
+		elif [ "$1" = "--exp" ]; then 
+			shift   
+#			gexp="$1"
+			tmpval="$1"
+			gexp=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"`
+			if ! expr "$gexp" : "[0-9\-]" > /dev/null ; then
+				printf "\nSpecify a number for exp, like --exp 0.1\n" 1>&2
+				printf "'$1' cannot be interpreted as a number..\n\n" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--ep" ]; then 
+			shift   
+#			aof="$1"
+			tmpval="$1"
+			aof=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"`
+			if ! expr "$aof" : "[0-9\-]" > /dev/null ; then
+				printf "\nSpecify a number for ep, like --ep 0.1\n" 1>&2
+				printf "'$1' cannot be interpreted as a number..\n\n" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--rop" ]; then 
+			shift   
+			rgop="$1"
+# Atode check
+		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" = "--strdir" ]; then
+			shift
+			strdir="$1"
+		elif [ "$1" = "--pdbidlist" ]; then
+			echo "--pdbidlist is temporarily unavailable, 2018/Dec." 1>&2
+			echo "" 1>&2
+			exit
+			shift
+			pdblist="$1"
+			if [ ! -e "$pdblist" ]; then
+				echo "Cannot open $pdblist" 1>&2
+				echo "" 1>&2
+				exit
+			fi
+		elif [ "$1" = "--pdbfilelist" ]; then
+			echo "--pdbfilelist is temporarily unavailable, 2018/Dec." 1>&2
+			echo "" 1>&2
+			exit
+			shift
+			ownlist="$1"
+			if [ ! -e "$ownlist" ]; then
+				echo "Cannot open $ownlist" 1>&2
+				echo "" 1>&2
+				exit
+			fi
+#		elif [ "$1" = "--enrich" ]; then
+#			enrich=1
+#			enrichseq=1
+#			enrichstr=1
+#			seektarget=""
+#		elif [ "$1" = "--enrichseq" ]; then
+#			enrich=1
+#			enrichseq=1
+#			enrichstr=0
+#			seektarget="-seq"
+#		elif [ "$1" = "--enrichstr" ]; then
+#			enrich=1
+#			enrichseq=0
+#			enrichstr=1
+#			seektarget="-str"
+		elif [ "$1" = "--dash" ]; then
+			newdash=1
+			if [ "$distance" != "local" -a "$distance" != "localgenaf" ]; then # 2021/Oct
+				distance="global"
+			fi
+			if [ "$iterate" -eq 0 ]; then # 2021/Oct
+				iterate=3
+			fi
+		elif [ "$1" = "--dashserver" ]; then
+			shift
+			dashserver="$1"
+		elif [ "$1" = "--originalseqonly" ]; then
+			newdash_originalsequenceonly=1
+		elif [ "$1" = "--excludehomologs" ]; then # works with --dash only
+			exclude_ho=1
+		elif [ "$1" = "--seedtable" ]; then
+			shift
+			seedtable="y"
+			seedtablefile="$1"
+		elif [ "$1" = "--seed" ]; then
+			shift
+			seed="m"
+			seedfiles="$seedfiles $1"
+		elif [ "$1" = "--minimumweight" ]; then
+			shift
+			minimumweight="$1"
+		elif [ "$1" = "--similaritylevel" ]; then
+			shift
+			similarityoffset="$1"
+		elif [ "$1" = "--unalignlevel" ]; then
+			shift
+			unalignlevel="$1"
+			unalignspecified=1
+		elif [ "$1" = "--skipiterate" ]; then
+			shift
+			fixthreshold="$1"
+		elif [ "$1" = "--bunkatsunashi" ]; then
+			bunkatsuopt=" -B "
+		elif [ "$1" = "--sp" ]; then
+			sprigorous=1
+		elif [ "$1" = "--focus" ]; then
+			focusarg=" -= "
+		elif [ "$1" = "--lhlimit" ]; then # atode namae henkou
+			shift
+			lhlimit=" -q $1 "
+		elif [ "$1" = "--sparsepickup" ]; then
+			shift
+			npickup="$1"
+		elif [ $progname = "fftns" -o  $progname = "nwns" ]; then
+			if [ "$1" -gt 0 ]; then
+				cycle=`expr "$1" - 0`
+			fi
+		else
+			echo "Unknown option:  $1" 1>&2
+			er=1;
+#			exit 1;
+		fi
+		shift   
+	done;
+
+
+#	echo "" 1>"$progressfile"
+
+	if [ $treeext = "memsavetree" ] || [ $treeext = "stepadd" ]; then
+		if [ $distance != "ktuples" ]; then  
+# auto -> memsave && globalpair ha erabarenai node, 
+# ~/maffttmp wo tsukau noha meijiteki ni shitei saretatoki dake.
+			if [ ! "$MAFFT_TMPDIR" ]; then  # space is acceptable, 2018/Mar/17
+				MAFFT_TMPDIR="$HOME/maffttmp"
+				mkdir -p "$MAFFT_TMPDIR" || exit
+			fi
+		fi
+	fi
+
+
+	if [ ! "$MAFFT_TMPDIR" ]; then
+		MAFFT_TMPDIR="$TMPDIR"
+	fi
+
+	TMPFILE=`env TMPDIR="$MAFFT_TMPDIR" mktemp -dt "$progname.XXXXXXXXXX"`
+	if [ $? -ne 0 ]; then
+		echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
+		mkdir -p "$MAFFT_TMPDIR/tmp" 1>&2
+		TMPFILE=`mktemp -d "$MAFFT_TMPDIR/tmp/$progname.XXXXXXXXXX"`
+	fi	
+
+#	lfs getstripe $TMPFILE  2>/dev/null && lfs setstripe -c 1 $TMPFILE # 2017/Oct
+	lfs getstripe "$TMPFILE" > /dev/null 2>&1 && lfs setstripe -c 1 "$TMPFILE" > /dev/null 2>&1 # 2018/Feb
+
+	if [ $os = "cygwin" ]; then
+		TMPFILE=`cygpath -w "$TMPFILE"`  # necessary to pass path to f2cl on cyswin, somehow unnecessary in msys.
+	fi
+
+#	umask 077  # 2021/Jan
+#	mkdir  "$TMPFILE"  || er=1
+
+
+function removetmpfile() { # for MPI
+	while true
+	do
+		rm -rf "$TMPFILE" && break
+		echo Retrying to remove "$TMPFILE". It may take several seconds. 1>&2
+		sleep 2
+	done
+}
+
+	if [ $debug -eq 1 ]; then
+#		trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0 # does not work in msys
+#		trap "tar cfv - $TMPFILE | gzip -c > debuginfo.tgz; rm -rf $TMPFILE " 0 15
+		trap "popd > /dev/null 2>&1; tar cfv - \"$TMPFILE\" | gzip -c > debuginfo.tgz; removetmpfile" 0 15
+	else
+#		trap "rm -rf $TMPFILE" 0 15
+		trap "removetmpfile" 0 15
+	fi
+	if [ $# -eq 1 ]; then
+		if [ -r "$1" -o "$1" = - ]; then
+
+			if [ -r "$addfile" ]; then
+				printf '';
+			else
+				echo "$0": Cannot open "$addfile". 1>&2
+				echo "" 1>&2
+				exit 1;
+			fi
+
+
+			cat "$1"              | tr "\r" "\n" > "$TMPFILE/infile"
+			echo ""                             >> "$TMPFILE/infile"
+			cat "$addfile"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_addfile"
+
+			if [ $dofilter -eq 1 ]; then
+#				mv "$TMPFILE/infile" "$TMPFILE/_tofilter"
+#				"$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/infile" 2>>"$progressfile" || exit 1
+				mv "$TMPFILE/_addfile" "$TMPFILE/_tofilter"
+				"$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/_addfile" 2>>"$progressfile" || exit 1
+			fi
+			cat "$TMPFILE/_addfile" >> "$TMPFILE/infile"
+
+			cat "$scorematrix"    | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_aamtx"
+			cat "$mergetable"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_subalignmentstable"
+			cat "$treeinfile"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_guidetree"
+			cat "$codonposfile"   | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_codonpos"
+			cat "$codonscorefile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_codonscore"
+			cat "$seedtablefile"  | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_seedtablefile"
+			cat "$laraparams"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_lara.params"
+			cat "$pdblist"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/pdblist"
+			cat "$ownlist"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/ownlist"
+			cat "$anchorfile"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_externalanchors"
+
+			SAVEIFS=$IFS
+# Fixed a bug: 'n' was misinterpreted as delimiter, 2020/Jun/19
+			IFS=$'\n'
+			filelist="$1
+$addfile
+$scorematrix
+$mergetable
+$treeinfile
+$codonposfile
+$codonscorefile
+$seedtablefile
+$laraparams
+$pdblist
+$ownlist"
+			for f in $filelist; do
+				file "$f" 2>/dev/null | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
+			done
+			IFS=$SAVEIFS
+
+#			echo $seedfiles
+			infilename="$1"
+			seedfilesintmp="/dev/null"
+			seednseq="0"
+			set $seedfiles > /dev/null
+			while [ $# -gt 1 ];
+			do
+				shift
+				if [ -r "$1" ]; then
+					cat "$1" | tr "\r" "\n" >  "$TMPFILE/seed$#"
+					file "$1" | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$1: UTF-16 or UTF-32?  Convert this file to ASCII\n\n" 1>&2 && exit 1;
+				else
+					echo "$0": Cannot open "$1". 1>&2
+					echo "" 1>&2
+					exit 1;
+				fi
+				seednseq=$seednseq" "`grep -c '^[>|=]' "$TMPFILE/seed$#"`
+				seedfilesintmp=$seedfilesintmp" "seed$#
+			done
+#			ls $TMPFILE
+#			echo $seedfilesintmp
+#			echo $seednseq
+
+
+		else
+			echo "$0": Cannot open "$1". 1>&2
+			echo "" 1>&2
+			er=1
+#			exit 1;
+		fi
+	else
+#		echo '$#'"=$#" 1>&2
+		er=1
+	fi
+
+
+	if [ $numthreads -lt 0 ]; then
+		if [ $os = "linux" ]; then
+			nlogicalcore=`cat /proc/cpuinfo | grep "^processor" | uniq | wc -l`
+			ncoresinacpu=`cat /proc/cpuinfo | grep 'cpu cores' | uniq | awk '{print $4}'`
+			nphysicalcpu=`cat /proc/cpuinfo | grep 'physical id' | sort | uniq | wc -l`
+			if [ $nlogicalcore -eq 0 ]; then
+				echo "Cannot get the number of processors from /proc/cpuinfo" 1>>"$progressfile"
+				exit 1
+			fi
+			if [ ${#ncoresinacpu} -gt 0 -a $nphysicalcpu -gt 0 ]; then
+				numthreads=`expr $ncoresinacpu '*' $nphysicalcpu`
+#				if [ $nlogicalcore -gt $numthreads ]; then    # Hyperthreading
+#					numthreads=`expr $numthreads '+' 1`
+#				fi
+			else
+				numthreads=$nlogicalcore
+			fi
+		elif [ $os = "darwin" ]; then
+			numthreads=`sysctl -n hw.physicalcpu`
+			if [ -z $numthreads ]; then
+				echo "Cannot get the number of physical cores from sysctl" 1>>"$progressfile"
+				exit 1
+			fi
+#			nlogicalcore=`sysctl -n hw.logicalcpu`
+#			if [ $nlogicalcore -gt $numthreads ]; then    # Hyperthreading
+#				numthreads=`expr $numthreads '+' 1`
+#			fi
+		elif [ "$windows" = "yes" ]; then
+#			numthreads=`wmic cpu get NumberOfCores | head -2 | tail -1 | awk '{print $1}'`
+			numthreads=`wmic cpu get NumberOfCores | awk 'BEGIN{n=0} {n+=$1} END{print n}'`
+
+		else
+			echo "Cannot count the number of physical cores." 1>>"$progressfile"
+			exit 1
+		fi
+		echo "OS = "$os 1>>"$progressfile"
+		echo "The number of physical cores = " $numthreads 1>>"$progressfile"
+	fi
+
+	if [ $numthreadstb -lt 0 ]; then
+		if [ $numthreads -lt 16 -o "$mpiscript" !=  "/dev/null" ]; then # mpi: museigen, multithread: 16 made
+#		if [ $numthreads -lt 31 ]; then
+			numthreadstb=$numthreads
+		else
+			numthreadstb=16
+		fi
+	fi
+
+	if [ $numthreadsit -lt 0 ]; then
+		if [ $numthreads -lt 8 ]; then
+			numthreadsit=$numthreads
+		else
+			numthreadsit=8
+		fi
+	fi
+
+	if [ $numthreadsit -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
+		echo 'Impossible' 1>&2;
+		exit 1;
+	fi
+
+
+	if [ "$addarg0" != " " ]; then
+
+#		iterate=0  # 2013/03/23 -> commented out, 2017/12
+		"$prefix/countlen" < "$TMPFILE/_addfile" > "$TMPFILE/addsize" 2>>"$progressfile"
+		nadd=`awk '{print $1}' "$TMPFILE/addsize"`
+		if [ $nadd -eq "0" ]; then
+			echo Check $addfile 1>&2
+			exit 1;
+		fi
+		if [ $seed != "x" -o $seedtable != "x" ]; then
+			echo 'Impossible' 1>&2;
+			echo 'Use either ONE of --seed, --seedtable, --addprofile and --add.' 1>&2
+			exit 1;
+		fi
+	else
+		nadd="0"
+	fi
+
+	if [ $auto -eq 1 ]; then
+		"$prefix/countlen" < "$TMPFILE/infile" > "$TMPFILE/size" 2>>"$progressfile"
+		nseq=`awk '{print $1}' "$TMPFILE/size"`
+		nlen=`awk '{print $3}' "$TMPFILE/size"`
+
+		if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then
+			distance="local"
+			iterate=1000
+			cycle=1
+			treeext="none"
+		elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then
+			distance="local"
+			iterate=2
+			cycle=1
+			treeext="none"
+		elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
+			distance="ktuples"
+			iterate=2
+			cycle=2
+			treeext="none"
+		elif [ $nseq -lt 20000 ]; then  # changed from 10000 2014/Oct/4
+			distance="ktuples"
+			iterate=0
+			cycle=2
+			treeext="none"
+		elif [ $nseq -lt 100000 ]; then  # changed from 50000 2017/Nov/24
+			distance="ktuples"
+			iterate=0
+			cycle=2
+			if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then
+				treeext="memsavetree"
+			fi
+		elif [ $nseq -lt 200000 ]; then  # changed from 90000 2017/Nov/24
+			distance="ktuples"
+			iterate=0
+			cycle=1
+			if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then
+				treeext="memsavetree"
+			fi
+		elif [ $nlen -lt 3000 ]; then
+			distance="parttree"
+			partdist="localalign"
+			algopt=" "
+			algoptit=" "
+#			algspecified=1
+			cycle=1
+		else
+			distance="parttree"
+			partdist="ktuples"
+			algopt=" "
+			algoptit=" "
+#			algspecified=1
+			cycle=1
+		fi
+
+
+#		if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then
+#			distance="local"
+#			iterate=1000
+#			cycle=1
+#		elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then
+#			distance="local"
+#			iterate=2
+#			cycle=1
+#		elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
+#			distance="ktuples"
+#			iterate=2
+#			cycle=2
+#		elif [ $nseq -lt 200000 ]; then
+#			distance="ktuples"
+#			iterate=0
+#			treeinopt=" -U "
+#			treein=1
+#			pileuporshuffle="a"
+#		elif [ $nlen -lt 3000 ]; then
+#			distance="parttree"
+#			partdist="localalign"
+#			algopt=" "
+#			algoptit=" "
+##			algspecified=1
+#			cycle=1
+#		else
+#			distance="parttree"
+#			partdist="ktuples"
+#			algopt=" "
+#			algoptit=" "
+##			algspecified=1
+#			cycle=1
+#		fi
+
+
+		if [ $fragment -ne 0 ]; then
+			norg=`expr $nseq '-' $nadd`
+			npair=`expr $norg '*' $nadd`
+			echo "nadd = " $nadd               1>>"$progressfile"
+			echo "npair = " $npair             1>>"$progressfile"
+			echo "nseq = " $nseq               1>>"$progressfile"
+			echo "nlen = " $nlen               1>>"$progressfile"
+
+			if [ $norg -eq 0 ]; then
+				echo "" 1>>"$progressfile"
+				echo "The reference sequence was removed because of ambiguous letters?" 1>>"$progressfile"
+				echo "" 1>>"$progressfile"
+				exit 1;
+			fi
+# nagasa check!
+#			if [ $npair -gt 10000000 -o $nlen -gt 5000 ]; then  # 2017/Oct 
+			if [ $npair -gt 10000000 -o $nlen -gt 5000 -o $nadd -gt 500000 ]; then  # 2021/Dec pairlocalalign to buntan
+				distance="ktuples"
+				echo "use ktuples, size=$tuplesize!" 1>>"$progressfile"
+#			elif [ $npair -gt 3000000 -o $nlen -gt 5000 ]; then  # 2017/Oct
+			elif [ $npair -gt 3000000 -o $nlen -gt 5000 ]; then  # 2017/Oct
+				distance="multi"
+				weighti="0.0"
+				echo "use multipair, weighti=0.0!" 1>>"$progressfile"
+			else
+				distance="multi"
+				echo "use multipair, weighti=$weighti!" 1>>"$progressfile"
+			fi
+			pairspecified=1
+		fi
+	fi
+
+	if [ `awk "BEGIN {print( 0.0+\"$sueff\" < 0.0 || 0.0+\"$sueff\" > 1.0 )}"` -gt 0 ]; then
+		printf "\n%s\n\n" "The argument of --mixedlinkage must be between 0.0 and 1.0" 1>>"$progressfile"
+		exit 1;
+	fi
+
+	if [ `awk "BEGIN {print( 0.0+\"$maxambiguous\" < 0.0 || 0.0+\"$maxambiguous\" > 1.0 )}"` -gt 0 ]; then
+		printf "\n%s\n\n" "The argument of --maxambiguous must be between 0.0 and 1.0" 1>>"$progressfile"
+		exit 1;
+	fi
+
+	if [ $allowshift -eq 1 ]; then
+		if [ $unalignspecified -ne 1 ]; then
+			unalignlevel="0.8"
+		fi
+		if [ $shiftpenaltyspecified -ne 1 ]; then
+			spfactor="2.00"
+		fi
+	fi
+
+	if [ $opdistspecified -ne 1 ]; then
+		gopdist=$gop
+	fi
+
+	if [ $unalignlevel != "0.0" -o `awk "BEGIN {print( 0.0+\"$spfactor\" < 100.0 )}"` -gt 0 ]; then
+		nmodel=" -: "
+		termgapopt=" "
+		if [ $distance = "localgenaf" ]; then
+			printf "\n%s\n" "The combination of --allowshift and --genafpair (E-INS-i/-1) is not supported." 1>>"$progressfile"
+			printf "%s\n" "Instead, please try --allowshift --globalpair (G-INS-i/-1 in the web version)," 1>>"$progressfile"
+			printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i/-1), too." 1>>"$progressfile"
+			exit 1;
+		fi
+		if [ $distance != "global" -o `awk "BEGIN {print( 0.0+\"$weighti\" < 1.0 )}"` -gt 0 ]; then
+			printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is supported only with the --globalpair option." 1>>"$progressfile"
+			exit 1;
+		fi
+		if [ $fragment -ne 0 ]; then
+			printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is not supported with the --addfragments option." 1>>"$progressfile"
+			exit 1;
+		fi
+	fi
+
+	if [ `awk "BEGIN {print( 0.0+\"$spfactor\" < 1.0 )}"` -gt 0 ]; then
+			printf "\n%s\n" "shiftpenalty must be >1." 1>>"$progressfile"
+			exit 1;
+	fi
+
+	if [ `awk "BEGIN {print( 0.0+\"$fixthreshold\" < 0.0 )}"` -gt 0 ]; then
+		printf "\n%s\n\n" "The 'fix' parameter must be >= 0.0" 1>>"$progressfile"
+		exit 1;
+	fi
+
+	if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" < 0.0 || 0.0+\"$unalignlevel\" > 1.0 )}"` -gt 0 ]; then
+		printf "\n%s\n\n" "The 'unalignlevel' parameter must be between 0.0 and 1.0" 1>>"$progressfile"
+		exit 1;
+	fi
+	if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" > 0.0 )}"` -gt 0 ]; then
+		laof="0"
+		lexp="0"
+		pgaof="0"
+		pgexp="0"
+		LEXP="0"
+		GEXP="0"
+		termgapopt=" "
+#		if [ $auto -eq 1 -o $fragment -ne 0 -o $iterate -gt 0 ]; then
+		if [ $fragment -ne 0 ]; then
+			printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported with the --addfragments option." 1>>"$progressfile"
+			exit 1;
+		fi
+		if [ $distance = "parttree" ]; then
+			printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported in the (dp)parttree option." 1>>"$progressfile"
+			exit 1;
+		fi
+		if [ $distance = "localgenaf" ]; then
+			printf "\n%s\n" "The --genafpair is not supported in the 'unalignlevel > 0' mode." 1>>"$progressfile"
+			printf "%s\n" "Instead, please try --unalignlevel xx --globalpair," 1>>"$progressfile"
+			printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i), too." 1>>"$progressfile"
+			exit 1;
+		fi
+#		if [ $distance != "ktuples" -a `awk "BEGIN {print( 0.0+\"$weighti\" > 0.0 )}"` -gt 0 -a $iterate -gt 0 ]; then
+#			printf "\n%s\n\n" "Please add --weighti 0.0, for now." 1>>"$progressfile"
+#			exit 1;
+#		fi
+	fi
+
+	if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" != 0.0 && 0.0+\"$unalignlevel\" != 0.0 )}"` -gt 0 ]; then
+		printf "\n%s\n\n" "Do not simultaneously specify --similaritylevel and --unalignlevel" 1>>"$progressfile"
+		exit 1;
+	fi
+
+	if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" < -1.0 || 0.0+\"$similarityoffset\" > 1.0 )}"` -gt 0 ]; then
+		printf "\n%s\n\n" "Similarity must be between -1.0 and +1.0" 1>>"$progressfile"
+		exit 1;
+	fi
+	aof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $aof}"`
+	laof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $laof}"`
+	pgaof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $pgaof}"`
+
+
+	if [ $parallelizationstrategy = "BESTFIRST" -o  $parallelizationstrategy = "BAATARI0" ]; then
+		iteratelimit=254
+	else
+		iteratelimit=16
+	fi
+	if [ $iterate -gt $iteratelimit ]; then    #??
+		iterate=$iteratelimit
+	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 $dafs -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
+
+#	if [ $algspecified -eq 0 ]; then
+#		if [ $distance = "parttree" ]; then 
+#			algopt=" -Q "
+#			algoptit=" "
+#		else
+#			algopt=" "
+#			algoptit=" "
+#		fi
+#	fi
+
+	if [ $sprigorous -eq 1 ]; then
+		algopt=" -@ "
+		if [ $iterate -gt 0 ]; then
+			if [ $numthreadsit -eq 0 ]; then
+				algoptit=" -@ -B -Z -z 1000 "
+			else
+				echo "" 1>>"$progressfile"
+				echo "At present, the combination of --sp and iterative refinement is supported only in a single thread." 1>>"$progressfile"
+				echo "Please try \"--thread -1 --threadit 0\", which runs the iterative refinment calculation on a single thread." 1>>"$progressfile"
+				echo "" 1>>"$progressfile"
+				exit 1;
+#				algoptit=" -@ -B -z 1000 "
+			fi
+		fi
+		termgapopt=" "
+		fft=0
+		memopt=" -N "
+	fi
+
+	model="$sbstmodel $kappa $fmodel $nmodel"
+
+	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 "  https://mafft.cbrc.jp/alignment/software/" 1>&2
+		echo "  MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)"        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 (fast)" 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 "--thread # :     Number of threads (if unsure, --thread -1)" 1>&2
+		echo "--dash :         Add structural information (Rozewicki et al, submitted)" 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 = "last" -o $distance = "lastmulti" ]; then
+		if [ ! -x "$prefix/lastal" -o ! -x "$prefix/lastdb" ]; then
+			echo ""       1>&2
+			echo "== Install LAST ============================================================" 1>&2
+			echo "LAST (Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487) is required." 1>&2
+			echo "http://last.cbrc.jp/"                                                       1>&2
+			echo "http://mafft.cbrc.jp/alignment/software/xxxxxxx.html "                      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" -o $mccaskill -eq 1 ]; then
+		if [ ! -x "$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://mafft.cbrc.jp/alignment/software/source.html "                1>&2
+			echo "==========================================================================" 1>&2
+			echo "" 1>&2
+			exit 1
+		fi
+	fi
+	if [ $distance = "dafs" -o $dafs -eq 1 ]; then
+		if [ ! -x "$prefix/dafs" ]; then
+			echo ""       1>&2
+			echo "== Install DAFS===========================================================" 1>&2
+			echo "DAFS (Sato et al. Journal 2012 issue:page) is required."                    1>&2
+			echo "http://www.ncrna.org/ "                                                     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
+		if [ $nodeout -eq 1 ]; then
+			treeoutopt="-^ -T"
+		else
+			treeoutopt="-t -T"
+		fi
+		iterate=0 
+		weighti="0.0"  # 2016Jul31, tbfast.c kara idou
+#		if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then # 2012/04, localpair --> local alignment distance
+#		if [ $distance = "global" ]; then
+#			distance="distonly"
+#		fi
+		if [ $treeout -eq 1 ]; then
+			parttreeoutopt="-t"
+			groupsize=1
+		else
+			parttreeoutopt=" "
+		fi
+		if [ $distout -eq 1 ]; then
+			distoutopt="-y ${distformat} -T"
+			if [ $treeout -eq 0 ]; then
+				treeoutopt=""
+			fi
+		fi
+	else
+		if [ $nodeout -eq 1 ]; then
+			if [ $iterate -gt 0 ]; then
+				echo "The --nodeout option supports only progressive method (--maxiterate 0) for now." 1>&2
+				exit 1
+			fi
+			parttreeoutopt="-t"
+			treeoutopt="-^"
+		elif [ $treeout -eq 1 ]; then
+			parttreeoutopt="-t"
+			treeoutopt="-t"
+		else
+			parttreeoutopt=" "
+			treeoutopt=" "
+		fi
+		if [ $distout -eq 1 ]; then
+			distoutopt="-y ${distformat}"
+		fi
+	fi
+#
+
+	formatcheck=`grep -c '^[[:blank:]]\+>' "$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 60000 -a $iterate -gt 1 ]; then   # 2014/Oct/22, test
+		echo "Too many sequences to perform iterative refinement!" 1>&2
+		echo "Please use a progressive method." 1>&2
+		exit 1
+	fi
+	if [ $distance = "lastmulti" -o $distance = "multi" ]; then
+		if [ $fragment -eq 0 ]; then
+			echo 'Specify --addfragments too' 1>&2
+			exit 1
+		fi
+	fi
+
+	if [ $fragment -ne 0 ]; then
+		if [ $pairspecified -eq 0 ]; then
+			distance="multi"
+		fi
+		if [ $distance != "multi" -a $distance != "hybrid" -a $distance != "lastmulti" -a $distance != "local" -a $distance != "last" -a  $distance != "ktuples" -a $distance != "ktuplesmulti" ]; then
+			echo 'Specify --multipair, --lastmultipair, --lastpair, --localpair, --6merpair, --6mermultipair or --hybridpair' 1>&2
+			exit 1
+		fi
+	fi
+
+	if [ "$memopt" = " -M -B " -a "$distance" != "ktuples" ]; then
+		echo "Impossible" 1>&2
+		exit 1
+	fi
+
+	if [ $distance = "parttree" ]; then
+		if [ "$mergetable" != "/dev/null" ]; then
+			echo "The combination of (dp)parttree and merge is Impossible.  " 1>&2
+			exit 1
+		fi
+		if [ $addfile != "/dev/null" ]; then
+			echo "The combination of (dp)parttree and add(fragments) is Impossible.  " 1>&2
+			exit 1
+		fi
+		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=" -U "    # -U -l -> fast 
+			cycle=1
+		elif [ $partdist = "fasta" ]; then
+			splitopt=" -S "
+			cycle=1
+		else
+			splitopt="  "
+		fi
+	fi
+
+
+	if [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed = "x" -a $seedtable = "x" -a $ownlist = "/dev/null" -a $pdblist = "/dev/null" -a $enrichstr -eq 0 -a $newdash -eq 0 \) ]; then
+		localparam=""
+		weighti="0.0"
+	elif [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed != "x" -o $seedtable != "x" -o $ownlist != "/dev/null" -o $pdblist != "/dev/null" -o $enrichstr -eq 1 -o $newdash -eq 1 \) ]; then
+		if [ $cycle -lt 2 ]; then
+			cycle=2                # disttbfast ha seed hi-taiou #  chuui 2014Aug21
+		fi
+		if [ $iterate -lt 2 ]; then
+			echo "############################################################################" 1>&2
+			echo "# Warning:" 1>&2
+			echo "#   Progressive alignment method is incompatible with the --seed option." 1>&2
+			echo "#   Automatically switched to the iterative refinement method." 1>&2
+			echo "#   " 1>&2
+			echo "# Also consider using the '--add' option, which is compatible with" 1>&2
+			echo "#   the progressive method and FASTER than the '--seed' option." 1>&2
+			echo "#   Usage is:" 1>&2
+			echo "#   % mafft --add newSequences existingAlignment > output" 1>&2
+			echo "############################################################################" 1>&2
+			iterate=2
+		fi
+		localparam="-l "$weighti
+	elif [ $distance = "parttree" ]; then
+		localparam=""
+		weighti="0.0"
+		if [ $groupsize -gt -1 ]; then
+			cycle=1
+		fi
+	else
+#		localparam="-B -l "$weighti   # weighti=0 demo bunkatsu nashi
+		localparam="-l "$weighti   # -B (bunkatsunashi) ha dvtditr.c de taiou (17/Jan/15)
+		if [ $cycle -gt 1 ]; then  # 09/01/08
+			cycle=1
+		fi
+	fi
+
+
+	if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+		aof="0.000"
+		if [ $oldgenafparam -ne 1 ]; then
+			laof="0.0"
+			lexp="0.0"
+#			LEXP="0.0" # default = 0.0
+			usenaivepairscore="-Z"
+		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 [ $f2clext = "-E" -a $anysymbol -gt 0 ]; then
+			echo '' 1>&2
+			echo 'The combination of --text and ( --anysymbol or --preservecase ) is impossible.' 1>&2
+			echo '' 1>&2
+			exit 1
+	fi
+
+#	if [ $f2clext = "-E" -a $scorematrix != "/dev/null" ]; then
+#			echo '' 1>&2
+#			echo 'At present, the combination of --text and (--aamatrix) is impossible.' 1>&2
+#			echo '' 1>&2
+#			exit 1
+#	fi
+
+	memsavetree=0
+	if [ $treeext != "none" ]; then
+		if [ $distance == "ktuples" ]; then
+			treein=1
+			treeinopt=" -U "
+			if [ $treeext == "randomchain" ]; then
+				echo "shuffle $randomseed" > "$TMPFILE/_guidetree"
+				cycle=1       #  disttbfast.c dem shitei
+			elif [ $treeext == "pileup" ]; then
+				echo "pileup" > "$TMPFILE/_guidetree"
+				cycle=1       #  disttbfast. shitei
+			elif [ $treeext == "memsavetree" ]; then
+				echo "very compact" > "$TMPFILE/_guidetree"
+				memsavetree=1
+			elif [ $treeext == "memsavetreex" ]; then
+				echo "compact " "$initialramusage" > "$TMPFILE/_guidetree"
+				memsavetree=1
+			elif [ $treeext == "stepadd" ]; then
+				echo "stepadd" > "$TMPFILE/_guidetree"
+				memsavetree=1
+			elif [ $treeext == "youngestlinkage" ]; then
+				echo "youngestlinkage" > "$TMPFILE/_guidetree"
+				memsavetree=1
+			else
+				echo "error in mafft.tmpl"
+				exit
+			fi
+		else # globalpair, localpair, genafpair, oldgenafpair
+#			treein, treeinopt ha kimaranai
+			if [ $treeext == "memsavetree" -o $treeext == "stepadd" ]; then
+				memsavetree=1
+			else
+				echo "With globalpair, localpair or genafpair," 1>>"$progressfile"
+				echo "Use --large, --minimumlinkage, --averagelinkage or --mixedlinkage." 1>>"$progressfile"
+				echo "--$treeext is supported only with --6merpair." 1>>"$progressfile"
+				echo '' 1>>"$progressfile"
+				exit
+			fi
+		fi
+		if [ $iterate -gt 0 ]; then
+			echo 'Iterative refinment is not supported for --large or --'$treeext  1>>"$progressfile"
+			echo '' 1>>"$progressfile"
+			exit 1
+		fi
+		if [ $fragment -ne 0 ]; then
+			echo '--addfragments, --addfull or --addlong is not yet supported for --large or --'$treeext  1>>"$progressfile"
+			echo "Use --add newsequences --$treeext" 1>>"$progressfile"
+			echo "Or, --addfragments (long, full) newsequences, without --"$treeext 1>>"$progressfile"
+			echo '' 1>>"$progressfile"
+			exit 1
+		fi
+		if [ "$mergetable" != "/dev/null" ]; then # 2018/Mar/2
+			echo '--merge is not yet supported for --large or --'$treeext  1>>"$progressfile"
+			echo "Use --merge without --"$treeext 1>>"$progressfile"
+			echo '' 1>>"$progressfile"
+			exit 1
+		fi
+	fi
+
+
+
+	if [ $nadd -gt "0" ]; then
+		if [ $fragment -eq "1" ]; then
+			addarg="$addarg0 $nadd -g -0.01"
+			addsinglearg=""
+			cycle=1 # chuui 2014Aug25
+			iterate=0
+		elif [ $fragment -eq "-1" ]; then
+			addarg="$addarg0 $nadd"
+			addsinglearg="-V"       # allowlongadds, 2014/04/02
+			cycle=1 # chuui 2014Aug25
+			iterate=0
+		elif [ $fragment -eq "-2" ]; then
+			addarg="$addarg0 $nadd"
+			addsinglearg="-V"       # allowlongadds + smoothing
+			add2ndhalfarg=$add2ndhalfarg" -p "
+			cycle=1 # chuui 2014Aug25
+			usenaivepairscore="-Z" # 2015Jun01
+			laof=0.0               # 2015Jun01
+			lexp=0.0               # 2015Jun01
+			iterate=0
+		elif [ $fragment -eq "-3" ]; then
+			addarg="$addarg0 $nadd"
+			addsinglearg="-x"       # add to top, 2021/12/31
+			cycle=1 # chuui 2014Aug25
+			iterate=0
+		elif [ $fragment -eq "-4" ]; then
+			addarg="$addarg0 $nadd"
+			addsinglearg="-s"       # add to root, 2023/2/11
+			cycle=1 # chuui 2014Aug25
+			iterate=0
+		else
+			addarg="$addarg0 $nadd"
+			addsinglearg=""
+#			iterate=1 # iterate ha shitei dori
+			bunkatsuopt=" -B "  # fftnsi demo bunktasu shinai
+			if [ "$add2ndhalfarg" != " " ]; then
+				if [ $auto -eq 1 -o $iterate -gt 0 ]; then
+#					echo '' 1>>"$progressfile"
+#					echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile"
+#					echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile"
+#					echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile"
+#					echo '' 1>>"$progressfile"
+#					exit 1
+					iterate=0
+				fi
+			fi
+		fi
+		
+
+#		cycle=1 # chuui 2014Aug19
+#		iterate=0
+#		treealg=" -q "  ## 2012/01/24  ## removed 2012/02/06
+	else
+		if [ "$add2ndhalfarg" != " " ]; then
+			echo '' 1>>"$progressfile"
+			echo 'The --keeplength and --mapout options are supported' 1>>"$progressfile"
+			echo 'only with --add, --addfragments or --addlong.' 1>>"$progressfile"
+			echo '' 1>>"$progressfile"
+			exit 1
+		fi
+	fi
+
+	if [ "$codonposfile" != "/dev/null" -o "$codonscorefile" != "/dev/null" ]; then
+		if [ $nadd -eq "0" -o $fragment -eq "0" ]; then
+			echo '' 1>>"$progressfile"
+			echo "'--codonpos' and '--codonscore' options are supported only with the '--6merpair --addfragments' option." 1>>"$progressfile"
+			echo '' 1>>"$progressfile"
+			exit 1
+		fi
+		if [ $distance != "ktuples" ]; then # ato de taiou
+			echo '' 1>>"$progressfile"
+			echo "'--codonpos' and '--codonscore' options are supported only with the '--6merpair --addfragments' option, at this point." 1>>"$progressfile"
+			echo '' 1>>"$progressfile"
+			exit 1
+		fi
+	fi
+
+
+	if [ -z "$localparam" -a $fragment -eq 0 -a $distance != "parttree" ]; then
+#		echo "use disttbfast"
+#		echo cycle = $cycle
+		cycletbfast=1            # tbfast wo jikkou shinai
+		cycledisttbfast=$cycle   # disttbfast ni -E cycle wo watasu
+		if [ $cycledisttbfast -eq 0 ]; then # --treeout de tsukau
+			cycledisttbfast=1
+		fi
+	else
+#		echo "use tbfast"
+#		echo cycle = $cycle
+		cycletbfast=$cycle       # 1 ijou nara jikkou
+		cycledisttbfast=1        # disttbfast ha ikkai dake
+	fi
+
+#	echo localparam=
+#	echo $localparam
+#	echo cycletbfast=
+#	echo $cycletbfast
+#	echo cycledisttbfast=
+#	echo $cycledisttbfast
+
+#exit
+
+	if [ $adjustdirection -gt 0 -a $seed != "x" ]; then
+			echo '' 1>&2
+			echo 'The combination of --adjustdirection(accurately) and --seed is not supported.' 1>&2
+			echo '' 1>&2
+			exit 1
+	fi
+
+
+	if [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+		if [ $distance = "ktuples" ]; then
+			echo 'Not supported.' 1>&2
+			echo 'Please add --globalpair, --localpair, --scarnapair, --dafspair' 1>&2
+			echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
+			exit 1
+		fi
+		if [ $f2clext = "-E" ]; then
+				echo '' 1>&2
+				echo 'For RNA alignment, the --text mode is impossible.' 1>&2
+				echo '' 1>&2
+				exit 1
+		fi
+	fi
+
+# cycle ga atode henkou sareru node koko de strategy no namae wo kimeru.
+# kokokara
+	if [ $treeext = "pileup" ]; then
+		strategy="Pileup-"
+	elif [ $treeext = "randomchain" ]; then
+		strategy="Randomchain-"
+	elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+		if [ $distance = "scarna" -o $distance = "dafs" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
+			strategy="X-"
+		elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
+			strategy="Q-"
+		fi
+	elif [ $distance = "fasta" -a $sw -eq 0 ]; then
+		strategy="F-"
+	elif [ $distance = "fasta" -a $sw -eq 1 ]; then
+		strategy="H-"
+	elif [ $distance = "blast" ]; then
+		strategy="B-"
+	elif [ $distance = "global" -o $distance = "distonly" ]; then
+		strategy="G-"
+	elif [ $distance = "local" ]; then
+		strategy="L-"
+	elif [ $distance = "last" ]; then
+		strategy="Last-"
+	elif [ $distance = "hybrid" ]; then
+		strategy="Hybrid-"
+	elif [ $distance = "multi" ]; then
+		strategy="Multi-"
+	elif [ $distance = "lastmulti" ]; then
+		strategy="LastMulti-"
+	elif [ $distance = "localgenaf" ]; then
+		strategy="E-"
+	elif [ $distance = "globalgenaf" ]; then
+		strategy="K-"
+	elif [ $fft -eq 1 ]; then
+		strategy="FFT-"
+	else
+		strategy="NW-"
+	fi
+	if [ $memsavetree -eq 1 ]; then
+		strategy=$strategy"large-"
+	fi
+#	if [ `echo "$weighti>0.0" | bc` -gt 0 ]; then
+	if [ `awk "BEGIN {print(0.0+\"$weighti\">0.0)}"` -gt 0 ]; then
+		strategy=$strategy"I"
+	fi
+	strategy=$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
+	elif [ $fragment -eq 1 ]; then
+		strategy=$strategy"fragment"
+	elif [ $fragment -eq -1 ]; then
+		strategy=$strategy"full"
+	elif [ $fragment -eq -2 ]; then
+		strategy=$strategy"long"
+	elif [ $fragment -eq -3 ]; then
+		strategy=$strategy"top"
+	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 $TMPFILE/order $f2clext "
+	elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
+		outputopt=" -c $strategy  $f2clext "
+	elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then
+		outputopt=" -y -r $TMPFILE/order "
+	elif [ $outputformat = "phylip" -a $outorder = "input" ]; then
+		outputopt=" -y "
+	elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
+		outputopt=" -f -l $linelength -r $TMPFILE/order "
+	else
+		outputopt="-f -l $linelength"
+	fi
+
+	if [ $newdash_originalsequenceonly -eq 1 ]; then
+		outputopt="$outputopt  -d "
+	fi
+# kokomade
+
+	
+	
+		pushd "$TMPFILE" > /dev/null
+
+		cat /dev/null > pre
+
+#		echo "nseq = " $nseq              1>>"$progressfile"
+#		echo "distance = " $distance      1>>"$progressfile"
+#		echo "iterate = " $iterate        1>>"$progressfile"
+#		echo "cycle = " $cycle            1>>"$progressfile"
+
+
+		if [ $anysymbol -eq 1 ]; then
+			mv infile orig
+			"$prefix/replaceu" $seqtype -i orig > infile 2>>"$progressfile" || exit 1
+		fi
+
+		if [ $mergetable != "/dev/null" ]; then
+			if [ $nadd -gt "0" ]; then
+				echo "Impossible" 1>&2
+				exit 1
+			fi
+#			if [ $seed != "x" -o $seedtable != "x" ]; then
+#				echo "This version does not support the combination of merge and seed." 1>&2
+#				exit 1
+#			fi
+#			iterate=0 # 2013/04/16
+			mergearg="-H $seedoffset"
+		fi
+
+		if [ $adjustdirection -gt 0 ]; then
+			if [ $fragment -ne 0 ]; then
+				fragarg="-F" #
+			else
+				fragarg="-F" # 2014/02/06, do not consider other additional sequences, even in the case of --add
+			fi
+			if [ $adjustdirection -eq 1 ]; then
+				"$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 5000 -o a > _direction 2>>"$progressfile"
+			elif [ $adjustdirection -eq 2 ]; then
+				"$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 100 -o a -d > _direction 2>>"$progressfile"
+			fi
+			"$prefix/setdirection" $mergearg -d _direction -i infile > infiled 2>>"$progressfile" || exit
+			mv infiled infile
+			if [ $anysymbol -eq 1 ]; then
+				"$prefix/setdirection" $mergearg -d _direction -i orig -r  > origd 2>>"$progressfile" || exit
+				mv origd orig
+			fi
+		fi
+
+		if [ $seed != "x" -o $seedtable != "x" ]; then
+			if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+				echo "The combination of --seed and (--pdbidlist or --pdbfilelist) is impossible."  1>>"$progressfile"
+				exit 1
+			fi
+#			if [ $enrich -eq 1 ]; then
+#				echo "The combination of --seed and (--enrich, --enrichseq or --enrichstr) is impossible at present."  1>>"$progressfile"
+#				exit 1
+#			fi
+
+			if [ $newdash -eq 1 ]; then
+				echo "The combination of --seed and --dash is impossible at present."  1>>"$progressfile"
+				exit 1
+			fi
+		fi
+
+
+#		if [ $enrich -eq 1 ]; then
+#			if [ $ownlist != "/dev/null" ]; then
+#				echo "Warning: Sequence homologs of the structures given with the --pdbfilelist option cannot be collected.\n" 1>>"$progressfile"
+#			fi
+#			echo "SEEKQUENCER (http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/) is" 1>>"$progressfile"
+#			if [ $pdblist != "/dev/null" ]; then
+#				echo "collecting homoplogs of the input sequences and the structures given with the --pdbidlist option." 1>>"$progressfile"
+#				perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -idf pdblist -out seekout -mod mafftash-split 2>>"seekerr"
+#				seekres="$?"
+#			else
+#				echo "collecting homologs of the input sequences." 1>>"$progressfile"
+#				perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -out seekout -mod mafftash-split 2>>"seekerr"
+#				seekres="$?"
+#			fi
+#			cat seekerr  1>>"$progressfile"
+#
+#			if [ $seekres -ne "0" ]; then
+#				echo "Error in SEEKQUENCER" 1>>"$progressfile"
+#				exit 1;
+#			fi
+#			echo "Done." 1>>"$progressfile"
+#
+#			if [ $enrichseq -eq 1 ]; then
+##				cat seekout.seq >> infile
+#				if [ $anysymbol -eq 1 ]; then
+#					"$prefix/replaceu" $seqtype -i seekout.seq -o $nseq >> infile
+#					cat seekout.seq >> orig
+#				else
+#					"$prefix/replaceu" $seqtype -i seekout.seq | sed 's/_os_[0-9]*_oe_//' >> infile
+#				fi
+#
+#			fi
+#			if [ $enrichstr -eq 1 ]; then
+#				nseekstr=`wc -l < seekout.str`
+#				if [ $nseekstr -gt 1 ]; then
+#					cat seekout.str >> pdblist
+#					pdblist="tsukaimasu"
+#				fi
+#			fi
+#		fi
+
+		if [ $seed != "x" ]; then
+			mv infile infile2
+			if [ $anysymbol -eq 1 ]; then
+				mv orig orig2
+				cat /dev/null > orig
+			fi
+			cat /dev/null > infile
+			cat /dev/null > hat3.seed
+			seedoffset=0
+#			echo "seednseq="$seednseq
+#			echo "seedoffset="$seedoffset
+			set $seednseq >> "$progressfile"
+#			echo $#
+			while [ $# -gt 1 ]
+			do
+				shift
+#				echo "num="$#
+
+				if [ $anysymbol -eq 1 ]; then
+					cat seed$# >> orig
+					"$prefix/replaceu" $seqtype -i seed$# -o $seedoffset > clean 2>>"$progressfile" || exit 1
+					mv clean seed$#
+				fi
+				"$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>>"$progressfile" || exit 1
+				cat hat3 >> hat3.seed
+#				echo "$1"
+				seedoffset=`expr $seedoffset + $1`
+#				echo "$1"
+#				echo "seedoffset="$seedoffset
+			done;
+#			echo "seedoffset="$seedoffset
+			if [ $anysymbol -eq 1 ]; then
+				"$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1  # yarinaoshi
+				cat orig2 >> orig
+			else
+				cat infile2 >> infile
+			fi
+		elif [ $seedtable != "x" ]; then
+			cat _seedtablefile > hat3.seed
+		elif [ $newdash -eq 1 ]; then
+			seemstobe=`"$prefix/countlen" -i infile | awk '{print $6}'`
+			if [ $seemstobe = "d" -a "x$seqtype" != "x-P" ]; then
+				echo "" 1>>"$progressfile"
+				echo "Error: This data seems to be nucleotide sequences." 1>>"$progressfile"
+				echo "Add the --amino flag if this is surely protein." 1>>"$progressfile"
+				echo "" 1>>"$progressfile"
+				exit 1;
+			fi
+			if [ $anysymbol -eq 1 ]; then
+				mv orig infile # replaceu wo mukouka
+			fi
+#			sed 's/-//g' infile > dashin # gap nozoku
+			awk '{if(/^>/)print; else {gsub( /-/,"" ); print;}}' infile > dashin
+
+			if [ ! -x "$prefix/dash_client" -o ! -x "$prefix/dash_client" ]; then
+				echo ""       1>&2
+				echo "== Install DASH client =====================================================" 1>&2
+				echo "To use this feature, uncomment the following line in Makefile"                1>&2
+				echo "DASH_CLIENT = dash_client"                                                    1>&2
+				echo "and re-compile the source."                                                   1>&2
+				echo "Note that it requires the 'Go' compiler."                                     1>&2
+				echo "============================================================================" 1>&2
+				echo "" 1>&2
+				exit 1
+			fi
+			
+			echo "Calling DASH (https://sysimm.org/dash/)" 1>>"$progressfile"
+			"$prefix/dash_client" -url "$dashserver" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile"
+			dashres="$?"
+			if [ $dashres -ne "0" ]; then
+				echo "Error in DASH" 1>>"$progressfile"
+				echo "To enable this feature, compile with DASH_CLIENT=dash_client. Go compiler is necessary." 1>>"$progressfile"
+				exit 1;
+			fi
+
+			if [ $exclude_ho -eq 1 ]; then # amari yokunai
+				awk 'BEGIN{out=1} !/^>_addedbymaffte_/{if(out) print; out=1} /^>_addedbymaffte_/{out=0}' dashsequences | sed 's/>DASH_/>DASH|/' > ho_excluded
+				mv ho_excluded dashsequences
+			fi
+
+			if [ "$mergetable" != "/dev/null" ]; then # 2020/Apr/30
+				ndash=`grep -c '>DASH_' dashsequences | head -1`
+#				echo "ndash = " $ndash
+				awk "{for( i=1;i<=NF;i++){if(0+\$i==0)break; printf( \"%d \", $ndash+\$i); } print \"\" }" _subalignmentstable > _subalignmentstableshifted
+				mv _subalignmentstableshifted _subalignmentstable
+				cp dashsequences dashsequences.bk
+				awk "BEGIN{nout=0} {if(\$1~/^>/) nout++; if( nout <= $ndash ) print;}" dashsequences > infile2
+				cat infile >> infile2
+				cp infile2 dashsequences
+			fi
+
+			sed 's/>DASH_/>DASH|/' dashsequences > renamed
+			mv renamed dashsequences
+			echo "Done." 1>>"$progressfile"
+#			cat  hat3.seed
+			seedoffset=`grep -c '^[>|=]' dashsequences | head -1 ` 
+			echo "# of structures = " 1>>"$progressfile"
+			echo $seedoffset 1>>"$progressfile"
+			if [ $anysymbol -eq 1 ]; then
+				cat dashsequences >> orig
+				"$prefix/replaceu" $seqtype -i dashsequences -o 0 > clean 2>>"$progressfile" || exit 1
+				mv clean infile
+
+#				"$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1  # yarinaoshi
+#				cat orig2 >> orig
+			else
+				cat dashsequences > infile
+#				cat infile2 >> infile
+			fi
+		else
+			cat /dev/null > hat3.seed
+		fi
+#		cat hat3.seed
+
+		if [ $mccaskill -eq 1 ]; then
+			"$prefix/mccaskillwrap" -s -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
+		elif [ $dafs -eq 1 ]; then
+			"$prefix/mccaskillwrap" -G -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
+		elif [ $contrafold -eq 1 ]; then
+			"$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
+		fi
+		if [ $distance = "fasta" ]; then
+			"$prefix/dndfast7" $swopt < infile > /dev/null  2>>"$progressfile"    || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hatx hat3
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "blast" ]; then
+			"$prefix/dndblast" < infile > /dev/null  2>>"$progressfile"      || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hatx hat3
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "foldalignlocal" ]; then
+			"$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -Q $spfactor -h $laof -H -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hatx hat3
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "foldalignglobal" ]; then
+			"$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hatx hat3
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "slara" ]; then
+			"$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop -Q $spfactor -T -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hatx hat3
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "lara" ]; then
+			"$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop -Q $spfactor -B -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hatx hat3
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "scarna" ]; then
+#			"$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -f $pggop -Q $spfactor -s -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
+#			cat hat3.seed hat3 > hatx
+#			mv hatx hat3
+#			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			"$prefix/tbfast" _  -C $numthreads $seqtype $model  -f $pggop -Q $spfactor -s -d "$prefix" _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "dafs" ]; then
+			"$prefix/pairlocalalign"  -C $numthreads $seqtype $model  -f $pggop -Q $spfactor -G -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hatx hat3
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "global" -a $memsavetree -eq 1 ]; then
+			if [ "$mpiscript" !=  "/dev/null" ]; then
+				sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof  -A  $usenaivepairscore $focusarg $treeinopt $treeoutopt  -i  infile > /dev/null 2>>"$progressfile" || exit 1
+			else
+				"$prefix/nodepair"  $lhlimit -u $unalignlevel $localparam  -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof  -A  $usenaivepairscore $focusarg $treeinopt $treeoutopt  -i  infile   > /dev/null 2>>"$progressfile" || exit 1
+			fi
+			echo 'nodepair' > _guidetree
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "local" -a $memsavetree -eq 1 ]; then
+			if [ "$mpiscript" !=  "/dev/null" ]; then
+				sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1
+			else
+				"$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile   > /dev/null 2>>"$progressfile" || exit 1
+			fi
+
+			echo 'nodepair' > _guidetree
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "localgenaf" -a $memsavetree -eq 1 ]; then
+			"$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null  2>>"$progressfile"      || exit 1
+			echo 'nodepair' > _guidetree
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "global" -a $memsavetree -eq 0 ]; then
+			"$prefix/tbfast" _  -u $unalignlevel $localparam  -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof  -A  $usenaivepairscore $focusarg  _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			
+		elif [ $distance = "local" -a $memsavetree -eq 0 ]; then
+			if [ $fragment -ne 0 ]; then 
+				"$prefix/pairlocalalign" $localparam $addarg   -C $numthreads $seqtype $model  -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore < infile > /dev/null  2>>"$progressfile"      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg  < infile   > /dev/null 2>>"$progressfile" || exit 1
+			else
+				"$prefix/tbfast" _  -u $unalignlevel $localparam -C $numthreads $seqtype $model  -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			fi
+		elif [ $distance = "globalgenaf" ]; then
+			"$prefix/pairlocalalign"  -u $unalignlevel $localparam -C $numthreads $seqtype $model  -g $pgexp -f $pggop -Q $spfactor -h $pgaof -O $GGOP -E $GEXP -K $usenaivepairscore < infile > /dev/null 2>>"$progressfile"    || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hatx hat3
+			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "localgenaf" -a $memsavetree -eq 0 ]; then
+			"$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null  2>>"$progressfile"      || exit 1
+		elif [ $distance = "last" ]; then
+			if [ $fragment -ne 0 ]; then 
+				"$prefix/pairlocalalign" $addarg   -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			else
+				"$prefix/pairlocalalign" -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
+#				addarg wo watasanai
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			fi
+		elif [ $distance = "lastmulti" ]; then
+			"$prefix/dndpre" -y $distformat $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof < infile > /dev/null 2>>"$progressfile"      || exit 1
+			mv hat2 hat2i
+			"$prefix/pairlocalalign" $addarg   -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -r $last_subopt $last_once -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hat2 hat2n
+			mv hatx hat3
+			if [ $fragment -ne 0 ]; then 
+				"$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			else
+				echo "Impossible" 1>&2
+				exit 1
+			fi
+		elif [ $distance = "multi" ]; then
+			"$prefix/dndpre" -y $distformat $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof  $usenaivepairscore < infile > /dev/null 2>>"$progressfile"      || exit 1
+			mv hat2 hat2i
+			"$prefix/pairlocalalign" $localparam $addarg   -C $numthreads $seqtype $model  -g $lexp -f $lgop -Q $spfactor -h $laof -Y $usenaivepairscore < infile > /dev/null  2>>"$progressfile"      || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hat2 hat2n
+			mv hatx hat3
+			if [ $fragment -ne 0 ]; then 
+				"$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			else
+				echo "Impossible" 1>&2
+				exit 1
+			fi
+		elif [ $distance = "hybrid" ]; then
+			"$prefix/pairlocalalign" $addarg   -C $numthreads $seqtype $model  -g $lexp -f $lgop -Q $spfactor -h $laof -Y < infile > /dev/null  2>>"$progressfile"      || exit 1
+			cat hat3.seed hat3 > hatx
+			mv hatx hat3
+			"$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			if [ $fragment -ne 0 ]; then 
+				"$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			else
+				"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			fi
+#		elif [ $distance = "distonly" ]; then
+#			"$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof  -t < infile > /dev/null  2>>"$progressfile"      || exit 1
+#			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+		elif [ $distance = "parttree" ]; then
+			"$prefix/splittbfast" $legacygapopt $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile   > pre 2>>"$progressfile" || exit 1
+			mv hat3.seed hat3
+		elif [ $distance = "ktuplesmulti" ]; then
+#			"$prefix/dndpre" -y $distformat $model -M 1 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof < infile > /dev/null 2>>"$progressfile"      || exit 1
+#			mv hat2 hat2i
+#			"$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
+#			mv hat2 hat2n
+			if [ $fragment -ne 0 ]; then 
+				"$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -d -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>>"$progressfile" || exit 1
+#				"$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			else
+				echo "Impossible" 1>&2
+				exit 1
+			fi
+		else
+			if [ $fragment -ne 0 ]; then 
+				"$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>>"$progressfile" || exit 1
+			else
+				"$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist  -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -g $gexp -f "-"$gop -Q $spfactor -h $aof  $param_fft $algopt $treealg $scoreoutarg $anchoropt -x $terminalmargin $oneiterationopt < infile   > pre 2>>"$progressfile" || exit 1
+				mv hat3.seed hat3
+			fi
+		fi
+		while [ $cycletbfast -gt 1 ]
+		do
+			if [ $distance = "parttree" ]; then
+				mv pre infile
+				"$prefix/splittbfast" $legacygapopt -Z $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  -p $partsize -s $groupsize $treealg $outnum -i infile   > pre 2>>"$progressfile" || exit 1
+			else
+				"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum -C $numthreadstb $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model  -f "-"$gop -Q $spfactor -h $aof $param_fft  $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>>"$progressfile" || exit 1
+# fragment>0 no baai, nanimoshinai
+# seed youchuui!!
+			fi
+			cycletbfast=`expr $cycletbfast - 1`
+		done
+		if [ $iterate -gt 0 ]; then
+			if [ $distance = "ktuples" ]; then
+			    "$prefix/dndpre" -y $distformat $seqtype $model -M 2 -C $numthreads < pre     > /dev/null 2>>"$progressfile" || exit 1
+			fi
+			"$prefix/dvtditr" -W $minimumweight $bunkatsuopt -E $fixthreshold -s $unalignlevel  $legacygapopt $mergearg $outnum -C $numthreadsit -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -Q $spfactor -h $aof  -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy  $scoreoutarg  -K $nadd < pre     > /dev/null 2>>"$progressfile" || exit 1
+		fi
+		if [ $coreout -eq 1 ]; then
+			"$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2
+			mv pre2 pre
+		elif [ $anysymbol -eq 1 ]; then
+			"$prefix/restoreu" $add2ndhalfarg -a pre -i orig > restored || exit 1
+			mv restored pre
+		fi
+
+
+
+
+		echo '' 1>>"$progressfile"
+		if [ $mccaskill -eq 1 ]; then
+			echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>>"$progressfile"
+			echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>>"$progressfile"
+			echo "incorporated in the iterative alignment process (4)." 1>>"$progressfile"
+			echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>>"$progressfile"
+			echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>>"$progressfile"
+			echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>>"$progressfile"
+			echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile"
+			echo "" 1>>"$progressfile"
+		elif [ $contrafold -eq 1 ]; then
+			echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>>"$progressfile"
+			echo "and then incorporated in the iterative alignment process (4)." 1>>"$progressfile"
+			echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>>"$progressfile"
+			echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile"
+			echo "" 1>>"$progressfile"
+		fi
+		if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+			echo "Input structures are decomposed into structural domains using" 1>>"$progressfile"
+			echo "Protein Domain Parser (Alexandrov & Shindyalov 2003)."         1>>"$progressfile"
+			echo "Domain pairs are aligned using the rash function in"           1>>"$progressfile"
+			echo "the ASH structural alignment package (Standley et al. 2007)."  1>>"$progressfile"
+		fi
+		if [ $pdblist != "/dev/null" ]; then
+			echo "Pre-computed alignments stored in "                            1>>"$progressfile"
+			echo "DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/) are used. "     1>>"$progressfile"
+		fi
+		if [ $distance = "fasta" -o $partdist = "fasta" ]; then
+			echo "Pairwise alignments were computed by FASTA" 1>>"$progressfile"
+			echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>>"$progressfile"
+		fi
+		if [ $distance = "blast" ]; then
+			echo "Pairwise alignments were computed by BLAST" 1>>"$progressfile"
+			echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>>"$progressfile"
+		fi
+		if [ $distance = "last" -o $distance = "lastmulti" ]; then
+			echo "Pairwise alignments were computed by LAST" 1>>"$progressfile"
+			echo "http://last.cbrc.jp/" 1>>"$progressfile"
+			echo "Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487" 1>>"$progressfile"
+		fi
+		if [ $distance = "scarna" ]; then
+			echo "Pairwise alignments were computed by MXSCARNA" 1>>"$progressfile"
+			echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>>"$progressfile"
+		fi
+		if [ $distance = "dafs" ]; then
+			echo "Pairwise alignments were computed by DAFS" 1>>"$progressfile"
+			echo "(Sato et al., 2012,,,,)." 1>>"$progressfile"
+		fi
+		if [ $distance = "lara" -o $distance = "slara" ]; then
+			echo "Pairwise alignments were computed by LaRA" 1>>"$progressfile"
+			echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>>"$progressfile"
+		fi
+		if [ $distance = "foldalignlocal" ]; then
+			echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>>"$progressfile"
+			echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile"
+		fi
+		if [ $distance = "foldalignglobal" ]; then
+			echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>>"$progressfile"
+			echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile"
+		fi
+#		printf "\n" 1>>"$progressfile"
+		echo 'Strategy:' 1>>"$progressfile"
+		printf ' '$strategy 1>>"$progressfile"
+		echo ' ('$performance')' 1>>"$progressfile"
+		echo ' '$explanation 1>>"$progressfile"
+		echo '' 1>>"$progressfile"
+		echo "If unsure which option to use, try 'mafft --auto input > output'." 1>>"$progressfile"
+		echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>>"$progressfile"
+		echo "" 1>>"$progressfile"
+		echo "The default gap scoring scheme has been changed in version 7.110 (2013 Oct)." 1>>"$progressfile"
+		echo "It tends to insert more gaps into gap-rich regions than previous versions." 1>>"$progressfile"
+		echo "To disable this change, add the --leavegappyregion option." 1>>"$progressfile"
+#		echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>>"$progressfile"
+#		echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>>"$progressfile"
+		if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+			echo "" 1>>"$progressfile"
+			if [ $oldgenafparam -eq 1 ]; then
+				echo "Obsolete parameters used for this calculation." 1>>"$progressfile"
+				echo "Also try the new parameters for E-INS-i, by not specifying --oldgenafpair." 1>>"$progressfile"
+			else
+				echo "Parameters for the E-INS-i option have been changed in version 7.243 (2015 Jun)." 1>>"$progressfile"
+				echo "To switch to the old parameters, use --oldgenafpair, instead of --genafpair." 1>>"$progressfile"
+			fi
+		fi
+		echo '' 1>>"$progressfile"
+
+		
+		if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
+#			cat dasherr >>"$progressfile"
+			echo '' >>"$progressfile"
+		fi
+
+	popd > /dev/null
+
+	if [ "$outputopt" != "-f -l -1" -o "$windows" = "yes" ]; then # Windows deha kaigyo code wo f2cl de modosu.
+#		ln -s "$TMPFILE/order" _order$$ # f2cl ga space ari filename ni taiou shiteinainode
+#		cp "$TMPFILE/order" _order$$ # ln -s no error wo sakeru
+		if [ "$outputfile" = "" ]; then
+			"$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" 2>"/dev/null" || exit 1
+		else
+			"$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" > "$outputfile" 2>"/dev/null" || exit 1
+		fi
+#		rm _order$$
+	else
+		if [ "$outputfile" = "" ]; then
+			cat < "$TMPFILE/pre" || exit 1
+		else
+			cat < "$TMPFILE/pre" > "$outputfile" || exit 1
+		fi
+	fi
+
+	if [ $treeout -eq 1 ]; then
+		cp "$TMPFILE/infile.tree" "$infilename.tree"
+	fi
+
+	if [ -s "$TMPFILE/GuideTree" ]; then # --merge no toki dake
+		cp "$TMPFILE/GuideTree" .
+	fi
+
+	if [ $distout -eq 1 ]; then
+		cp "$TMPFILE/${distformat}" "$infilename.${distformat}"
+	fi
+
+	if [ $npickup -ne 0 ]; then
+		cp "$TMPFILE/notused" "$infilename.notused"
+	fi
+
+	if [ -s "$TMPFILE/_deletemap" ]; then
+		if [ "$mapoutfile" = "/dev/null" ]; then
+			cp "$TMPFILE/_deletemap" "$addfile.map"
+		else
+			cp "$TMPFILE/_deletemap" "$mapoutfile"
+		fi
+	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="$tmpawk"
+#fi
+# 2017/May/12, Windows no gawk wo sakeru tame
+
+#echo "prog="$prog 1>&2
+
+umask 077
+(
+$prog '
+BEGIN {
+	prefix = ENVIRON["prefix"];
+	version = ENVIRON["version"];
+	myself = ENVIRON["myself"];
+	pwd = ENVIRON["mafft_working_dir"];  # from mafft.bat on windows
+	if( pwd == "" ) pwd = ENVIRON["PWD"];
+	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) 2002- Kazutaka Katoh\n" )                                 > "/dev/tty";
+		printf( "        MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)\n" )                     > "/dev/tty";
+		printf( "        https://mafft.cbrc.jp/alignment/software/\n" )                           > "/dev/tty";
+		printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
+		printf( "\n" ) > "/dev/tty";
+	
+		while( 1 )
+		{
+			printf( "\n" ) > "/dev/tty";
+			printf( "Input file? (FASTA format; Folder=%s)\n@ ", pwd ) > "/dev/tty";
+			res = getline < "/dev/tty";
+			close( "/dev/tty" )
+			if( res == 0 || NF == 0 )
+				continue;
+			infile = sprintf( "%s", $0 );
+	
+			res = getline < infile;
+			close( infile );
+			if( res == -1 )
+			{
+				printf( "%s: No such file.\n\n", infile ) > "/dev/tty";
+				printf( "Filename extension (eg., .txt) must be typed, if any.\n\n" ) > "/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", $0 );
+				printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
+				break;
+			}
+		}
+	
+		while( 1 )
+		{
+			outargs = "";
+			printf( "\n" ) > "/dev/tty";
+			printf( "Output format?\n" ) > "/dev/tty";
+			printf( "  1. Clustal format / Sorted\n" ) > "/dev/tty";
+			printf( "  2. Clustal format / Input order\n" ) > "/dev/tty";
+			printf( "  3. Fasta format   / Sorted\n" ) > "/dev/tty";
+			printf( "  4. Fasta format   / Input order\n" ) > "/dev/tty";
+			printf( "  5. Phylip format  / Sorted\n" ) > "/dev/tty";
+			printf( "  6. Phylip format  / Input order\n" ) > "/dev/tty";
+			printf( "@ " ) > "/dev/tty";
+			res = getline < "/dev/tty";
+			close( "/dev/tty" );
+#			printf( "res=%d, NF=%d\n", res, NF );
+
+			resnum = 0 + $1;
+#			printf( "resnum=%d\n", resnum );
+
+			if( resnum < 1 || 6 < resnum )
+				continue;
+			else
+			{
+				if( resnum == 1 )
+					outargs = "--clustalout --reorder";
+				else if( resnum == 2 )
+					outargs = "--clustalout --inputorder";
+				else if( resnum == 3 )
+					outargs = "--reorder";
+				else if( resnum == 4 )
+					outargs = "--inputorder";
+				else if( resnum == 5 )
+					outargs = "--phylipout --reorder";
+				else if( resnum == 6 )
+					outargs = "--phylipout --inputorder";
+				else
+					continue;
+				printf( "OK. arguments = %s\n\n", outargs ) > "/dev/tty";
+				break;
+			}
+		}
+	
+		while( 1 )
+		{
+			arguments = "";
+			printf( "\n" ) > "/dev/tty";
+			printf( "Strategy?\n" ) > "/dev/tty";
+			printf( "  1. --auto\n" ) > "/dev/tty";
+			printf( "  2. FFT-NS-1 (fast)\n" ) > "/dev/tty";
+			printf( "  3. FFT-NS-2 (default)\n" ) > "/dev/tty";
+			printf( "  4. G-INS-i  (accurate)\n" ) > "/dev/tty";
+			printf( "  5. L-INS-i  (accurate)\n" ) > "/dev/tty";
+			printf( "  6. E-INS-i  (accurate)\n" ) > "/dev/tty";
+			printf( "@ " ) > "/dev/tty";
+			res = getline < "/dev/tty";
+			close( "/dev/tty" );
+#			printf( "res=%d, NF=%d\n", res, NF );
+
+			resnum = 0 + $1;
+#			printf( "resnum=%d\n", resnum );
+
+			if( resnum < 1 || 6 < resnum )
+				continue;
+			else
+			{
+				if( resnum == 1 )
+					arguments = "--auto";
+				else if( resnum == 2 )
+					arguments = "--retree 1";
+				else if( resnum == 3 )
+					arguments = "--retree 2";
+				else if( resnum == 4 )
+					arguments = "--globalpair --maxiterate 16";
+				else if( resnum == 5 )
+					arguments = "--localpair  --maxiterate 16";
+				else if( resnum == 6 )
+					arguments = "--genafpair  --maxiterate 16";
+				else
+					arguments = sprintf( "%s", $0 );
+				printf( "OK. arguments = %s %s\n\n", arguments, outargs ) > "/dev/tty";
+				break;
+			}
+		}
+
+
+		while( 1 )
+		{
+			printf( "\n" ) > "/dev/tty";
+			printf( "Additional arguments? (--ep # --op # --kappa # etc)\n" ) > "/dev/tty";
+			printf( "@ " ) > "/dev/tty";
+			res = getline < "/dev/tty";
+			close( "/dev/tty" );
+			if( res == 0 || NF == 0 )
+			{
+				break;
+			}
+			else
+			{
+				addargs = sprintf( "%s", $0 );
+				printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty";
+				break;
+			}
+		}
+
+		arguments = sprintf( "%s %s %s", addargs, arguments, outargs );
+
+		print ""
+		command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile );
+		gsub( /\\/, "/", command );
+
+
+		printf( "command=\n%s\n", command ) > "/dev/tty";
+	
+	
+		while( 1 )
+		{
+			go = 0;
+			printf( "Type Y or just enter to run this command.\n" ) > "/dev/tty";
+			printf( "@ " ) > "/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 );
+	command = sprintf( "more \"%s\"", outfile );
+	system( command );
+	printf( "Press Enter to exit." ) > "/dev/tty";
+	res = getline < "/dev/tty";
+}
+'
+)
+exit 0;