From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Tue, 21 Jun 2011 10:57:18 +0000 (+0000)
Subject: New Mafft binaries for 64 bit linux system
X-Git-Url: http://source.jalview.org/gitweb/?p=jabaws.git;a=commitdiff_plain;h=a65c48a75f164b6ad0e577bd33168904328ce625

New Mafft binaries for 64 bit linux system

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4288 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/binaries/linuxAMD64/mafft/contrafoldwrap b/binaries/linuxAMD64/mafft/contrafoldwrap
index 39bf811..d08b233 100644
Binary files a/binaries/linuxAMD64/mafft/contrafoldwrap and b/binaries/linuxAMD64/mafft/contrafoldwrap differ
diff --git a/binaries/linuxAMD64/mafft/countlen b/binaries/linuxAMD64/mafft/countlen
index dcfe8a8..6813415 100644
Binary files a/binaries/linuxAMD64/mafft/countlen and b/binaries/linuxAMD64/mafft/countlen differ
diff --git a/binaries/linuxAMD64/mafft/disttbfast b/binaries/linuxAMD64/mafft/disttbfast
index 33d25a3..f874945 100644
Binary files a/binaries/linuxAMD64/mafft/disttbfast and b/binaries/linuxAMD64/mafft/disttbfast differ
diff --git a/binaries/linuxAMD64/mafft/dndblast b/binaries/linuxAMD64/mafft/dndblast
index 2427b3a..ce94114 100644
Binary files a/binaries/linuxAMD64/mafft/dndblast and b/binaries/linuxAMD64/mafft/dndblast differ
diff --git a/binaries/linuxAMD64/mafft/dndfast7 b/binaries/linuxAMD64/mafft/dndfast7
index d632041..0d5ec67 100644
Binary files a/binaries/linuxAMD64/mafft/dndfast7 and b/binaries/linuxAMD64/mafft/dndfast7 differ
diff --git a/binaries/linuxAMD64/mafft/dndpre b/binaries/linuxAMD64/mafft/dndpre
index 119bbe9..3490c6d 100644
Binary files a/binaries/linuxAMD64/mafft/dndpre and b/binaries/linuxAMD64/mafft/dndpre differ
diff --git a/binaries/linuxAMD64/mafft/dndpre2 b/binaries/linuxAMD64/mafft/dndpre2
index 8cc8e67..f75796d 100644
Binary files a/binaries/linuxAMD64/mafft/dndpre2 and b/binaries/linuxAMD64/mafft/dndpre2 differ
diff --git a/binaries/linuxAMD64/mafft/dvtditr b/binaries/linuxAMD64/mafft/dvtditr
index 90036dc..2c138ab 100644
Binary files a/binaries/linuxAMD64/mafft/dvtditr and b/binaries/linuxAMD64/mafft/dvtditr differ
diff --git a/binaries/linuxAMD64/mafft/f2cl b/binaries/linuxAMD64/mafft/f2cl
index 7509d1e..6a76dcc 100644
Binary files a/binaries/linuxAMD64/mafft/f2cl and b/binaries/linuxAMD64/mafft/f2cl differ
diff --git a/binaries/linuxAMD64/mafft/getlag b/binaries/linuxAMD64/mafft/getlag
index 645ff71..5a8a5fe 100644
Binary files a/binaries/linuxAMD64/mafft/getlag and b/binaries/linuxAMD64/mafft/getlag differ
diff --git a/binaries/linuxAMD64/mafft/mafft b/binaries/linuxAMD64/mafft/mafft
new file mode 100644
index 0000000..16b6660
--- /dev/null
+++ b/binaries/linuxAMD64/mafft/mafft
@@ -0,0 +1,1658 @@
+#! /bin/sh
+
+
+er=0;
+myself=`dirname "$0"`/`basename "$0"`; export myself
+version="v6.857b (2011/05/30)"; export version
+LANG=C; export LANG
+os=`uname`
+progname=`basename "$0"`
+if [ `echo $os | grep -i cygwin` ]; then
+	os="cygwin"
+elif [ `echo $os | grep -i darwin` ]; then
+	os="darwin"
+elif [ `echo $os | grep -i sunos` ]; then
+	os="sunos"
+elif [ `echo $os | grep -i linux` ]; then
+	os="linux"
+else
+	os="unix"
+fi
+export os
+
+if [ "$MAFFT_BINARIES" ]; then
+	prefix="$MAFFT_BINARIES"
+else
+	prefix=/usr/libexec/mafft
+fi
+export prefix
+
+if [ $# -gt 0 ]; then
+	if [ "$1" = "--man" ]; then 
+		man "$prefix/mafft.1"
+		exit 0;
+	fi
+fi
+
+if [ ! -x "$prefix/tbfast" ]; then
+	echo "" 1>&2
+	echo "correctly installed?" 1>&2
+	echo "mafft binaries have to be installed in \$MAFFT_BINARIES" 1>&2
+	echo "or the $prefix directory". 1>&2
+	echo "" 1>&2
+	exit 1
+	er=1
+fi
+
+defaultiterate=0
+defaultcycle=2
+defaultgop="1.53"
+#defaultaof="0.123"
+defaultaof="0.000"
+defaultlaof="0.100"
+defaultlgop="-2.00"
+defaultfft=1
+defaultrough=0
+defaultdistance="sixtuples"
+#defaultdistance="local"
+defaultweighti="2.7"
+defaultweightr="0.0"
+defaultweightm="1.0"
+defaultmccaskill=0
+defaultcontrafold=0
+defaultalgopt="  "
+defaultalgoptit="  "
+defaultsbstmodel=" -b 62 "
+defaultfmodel=" "
+defaultkappa=" "
+if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then
+	defaultfft=1
+	defaultcycle=1
+	defaultiterate=1000
+	defaultdistance="scarna"
+	defaultweighti="3.2"
+	defaultweightr="8.0"
+	defaultweightm="2.0"
+	defaultmccaskill=1
+	defaultcontrafold=0
+	defaultalgopt=" -A "
+	defaultalgoptit=" -AB " ## chui
+	defaultaof="0.0"
+	defaultsbstmodel=" -b 62 "
+	defaultkappa=" "
+	defaultfmodel=" -a "
+elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
+	defaultfft=1
+	defaultcycle=1
+	defaultiterate=1000
+	defaultdistance="global"
+	defaultweighti="3.2"
+	defaultweightr="8.0"
+	defaultweightm="2.0"
+	defaultmccaskill=1
+	defaultcontrafold=0
+	defaultalgopt=" -A "
+	defaultalgoptit=" -AB " ## chui
+	defaultaof="0.0"
+	defaultsbstmodel=" -b 62 "
+	defaultkappa=" "
+	defaultfmodel=" -a "
+elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
+	defaultfft=0
+	defaultcycle=1
+	defaultiterate=1000
+	defaultdistance="local"
+elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then
+	defaultfft=1
+	defaultcycle=1
+	defaultiterate=1000
+	defaultdistance="global"
+elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then
+	defaultfft=0
+	defaultcycle=1
+	defaultiterate=1000
+	defaultdistance="localgenaf"
+elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
+	defaultfft=1
+	defaultcycle=2
+	defaultdistance="sixtuples"
+elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
+	defaultfft=1
+	defaultcycle=2
+	defaultiterate=2
+	defaultdistance="sixtuples"
+elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
+	defaultfft=0
+	defaultcycle=2
+	defaultdistance="sixtuples"
+elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
+	defaultfft=0
+	defaultcycle=2
+	defaultiterate=2
+	defaultdistance="sixtuples"
+fi
+outputfile=""
+namelength=15
+anysymbol=0
+parallelizationstrategy="BAATARI2"
+kappa=$defaultkappa
+sbstmodel=$defaultsbstmodel
+fmodel=$defaultfmodel
+gop=$defaultgop
+aof=$defaultaof
+cycle=$defaultcycle
+iterate=$defaultiterate
+fft=$defaultfft
+rough=$defaultrough
+distance=$defaultdistance
+forcefft=0
+memopt=" "
+weightopt=" "
+GGOP="-6.00"
+LGOP="-6.00"
+LEXP="-0.000"
+GEXP="-0.000"
+lgop=$defaultlgop
+lexp="-0.100"
+laof=$defaultlaof
+pggop="-2.00"
+pgexp="-0.10"
+pgaof="0.10"
+rgop="-1.530"
+rgep="-0.000"
+seqtype="  "
+weighti=$defaultweighti
+weightr=$defaultweightr
+weightm=$defaultweightm
+rnaalifold=0
+mccaskill=$defaultmccaskill
+contrafold=$defaultcontrafold
+quiet=0
+debug=0
+sw=0
+algopt=$defaultalgopt
+algoptit=$defaultalgoptit
+scorecalcopt=" "
+coreout=0
+corethr="0.5"
+corewin="100"
+coreext=" "
+outputformat="pir"
+outorder="input"
+seed="x"
+seedtable="x"
+auto=0
+groupsize=-1
+partsize=50
+partdist="sixtuples"
+partorderopt=" -x "
+treeout=0
+distout=0
+treein=0
+topin=0
+treeinopt="  "
+seedfiles="/dev/null"
+seedtablefile="/dev/null"
+aamatrix="/dev/null"
+treeinfile="/dev/null"
+rnascoremtx=" "
+laraparams="/dev/null"
+foldalignopt=" "
+treealg=" -X "
+scoreoutarg=" "
+numthreads=0
+randomseed=0
+addfile="/dev/null"
+addarg0=" "
+outnum=" "
+if [ $# -gt 0 ]; then
+	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" = "--algq" ]; then 
+			algopt=" -Q "
+			algoptit=" -QB "
+		elif [ "$1" = "--namelength" ]; then 
+			shift   
+			namelength=`expr "$1" - 0`
+		elif [ "$1" = "--groupsize" ]; then 
+			shift   
+			groupsize=`expr "$1" - 0`
+		elif [ "$1" = "--partsize" ]; then 
+			shift   
+			partsize=`expr "$1" - 0`
+		elif [ "$1" = "--parttree" ]; then 
+			distance="parttree"
+			partdist="sixtuples"
+		elif [ "$1" = "--dpparttree" ]; then 
+			distance="parttree"
+			partdist="localalign"
+		elif [ "$1" = "--fastaparttree" ]; then 
+			distance="parttree"
+			partdist="fasta"
+		elif [ "$1" = "--treeout" ]; then 
+			treeout=1
+		elif [ "$1" = "--distout" ]; then 
+			distout=1
+		elif [ "$1" = "--fastswpair" ]; then
+			distance="fasta"
+			sw=1
+		elif [ "$1" = "--fastapair" ]; then
+			distance="fasta"
+			sw=0
+		elif [ "$1" = "--averagelinkage" ]; then
+			treealg=" -E "
+		elif [ "$1" = "--minimumlinkage" ]; then
+			treealg=" -q "
+		elif [ "$1" = "--noscore" ]; then
+			scorecalcopt=" -Z "
+		elif [ "$1" = "--6merpair" ]; then
+			distance="sixtuples"
+		elif [ "$1" = "--blastpair" ]; then
+			distance="blast"
+		elif [ "$1" = "--globalpair" ]; then
+			distance="global"
+		elif [ "$1" = "--localpair" ]; then
+			distance="local"
+		elif [ "$1" = "--scarnapair" ]; then
+			distance="scarna"
+		elif [ "$1" = "--larapair" ]; then
+			distance="lara"
+		elif [ "$1" = "--slarapair" ]; then
+			distance="slara"
+		elif [ "$1" = "--foldalignpair" ]; then
+			distance="foldalignlocal"
+		elif [ "$1" = "--foldalignlocalpair" ]; then
+			distance="foldalignlocal"
+		elif [ "$1" = "--foldalignglobalpair" ]; then
+			distance="foldalignglobal"
+		elif [ "$1" = "--globalgenafpair" ]; then
+			distance="globalgenaf"
+		elif [ "$1" = "--localgenafpair" ]; then
+			distance="localgenaf"
+		elif [ "$1" = "--genafpair" ]; then
+			distance="localgenaf"
+		elif [ "$1" = "--memsave" ]; then
+			memopt=" -M -B "         # -B (bunkatsunashi no riyu ga omoidasenai)
+		elif [ "$1" = "--nomemsave" ]; then
+			memopt=" -N "
+		elif [ "$1" = "--nuc" ]; then 
+			seqtype=" -D "
+		elif [ "$1" = "--amino" ]; then 
+			seqtype=" -P "
+		elif [ "$1" = "--fft" ]; then 
+			fft=1
+			forcefft=1
+		elif [ "$1" = "--nofft" ]; then 
+			fft=0
+		elif [ "$1" = "--quiet" ]; then 
+			quiet=1
+		elif [ "$1" = "--debug" ]; then 
+			debug=1
+		elif [ "$1" = "--coreext" ]; then 
+			coreext=" -c "
+		elif [ "$1" = "--core" ]; then 
+			coreout=1
+		elif [ "$1" = "--out" ]; then 
+			shift   
+			outputfile="$1"
+		elif [ "$1" = "--thread" ]; then 
+			shift
+			numthreads=`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 
+			scoreoutarg="-n"
+		elif [ "$1" = "--addprofile" ]; then 
+			shift   
+			addarg0="-I"
+			addfile="$1"
+		elif [ "$1" = "--add" ]; then 
+			shift   
+			addarg0="-K -I"
+			addfile="$1"
+		elif [ "$1" = "--maxiterate" ]; then 
+			shift   
+			iterate=`expr "$1" - 0` 
+		elif [ "$1" = "--retree" ]; then 
+			shift   
+			cycle=`expr "$1" - 0`
+		elif [ "$1" = "--aamatrix" ]; then 
+			shift   
+			sbstmodel=" -b -1 "
+			aamatrix="$1"
+		elif [ "$1" = "--treein" ]; then 
+			shift   
+			treeinopt=" -U "
+			treein=1
+			treeinfile="$1"
+		elif [ "$1" = "--topin" ]; then 
+			shift   
+			treeinopt=" -V "
+			treein=1
+			treeinfile="$1"
+			echo "The --topin option has been disabled." 1>&2
+			echo "There was a bug in version < 6.530."   1>&2
+			echo "This bug has not yet been fixed."      1>&2
+			exit 1
+		elif [ "$1" = "--kappa" ]; then 
+			shift   
+			kappa=" -k $1 "
+		elif [ "$1" = "--fmodel" ]; then 
+			fmodel=" -a "
+		elif [ "$1" = "--jtt" ]; then 
+			shift   
+			sbstmodel=" -j $1"
+		elif [ "$1" = "--kimura" ]; then 
+			shift   
+			sbstmodel=" -j $1"
+		elif [ "$1" = "--tm" ]; then 
+			shift   
+			sbstmodel=" -m $1"
+		elif [ "$1" = "--bl" ]; then 
+			shift   
+			sbstmodel=" -b $1"
+		elif [ "$1" = "--weighti" ]; then
+			shift   
+			weighti="$1"
+		elif [ "$1" = "--weightr" ]; then
+			shift   
+			weightr="$1"
+		elif [ "$1" = "--weightm" ]; then
+			shift   
+			weightm="$1"
+		elif [ "$1" = "--rnaalifold" ]; then
+			rnaalifold=1
+		elif [ "$1" = "--mccaskill" ]; then
+			mccaskill=1
+			contrafold=0
+		elif [ "$1" = "--contrafold" ]; then
+			mccaskill=0
+			contrafold=1
+		elif [ "$1" = "--ribosum" ]; then
+			rnascoremtx=" -s "
+		elif [ "$1" = "--op" ]; then 
+			shift   
+			gop="$1"
+		elif [ "$1" = "--ep" ]; then 
+			shift   
+			aof="$1"
+		elif [ "$1" = "--rop" ]; then 
+			shift   
+			rgop="$1"
+		elif [ "$1" = "--rep" ]; then 
+			shift   
+			rgep="$1"
+		elif [ "$1" = "--lop" ]; then 
+			shift   
+			lgop="$1"
+		elif [ "$1" = "--LOP" ]; then 
+			shift   
+			LGOP="$1"
+		elif [ "$1" = "--lep" ]; then 
+			shift   
+			laof="$1"
+		elif [ "$1" = "--lexp" ]; then 
+			shift   
+			lexp="$1"
+		elif [ "$1" = "--LEXP" ]; then 
+			shift   
+			LEXP="$1"
+		elif [ "$1" = "--GEXP" ]; then 
+			shift   
+			GEXP="$1"
+		elif [ "$1" = "--GOP" ]; then 
+			shift   
+			GGOP="$1"
+		elif [ "$1" = "--gop" ]; then 
+			shift   
+			pggop="$1"
+		elif [ "$1" = "--gep" ]; then 
+			shift   
+			pgaof="$1"
+		elif [ "$1" = "--gexp" ]; then 
+			shift   
+			pgexp="$1"
+		elif [ "$1" = "--laraparams" ]; then 
+			shift   
+			laraparams="$1"
+		elif [ "$1" = "--corethr" ]; then 
+			shift   
+			corethr="$1"
+		elif [ "$1" = "--corewin" ]; then 
+			shift   
+			corewin="$1"
+		elif [ "$1" = "--seedtable" ]; then
+			shift
+			seedtable="y"
+			seedtablefile="$1"
+		elif [ "$1" = "--seed" ]; then
+			shift
+			seed="m"
+			seedfiles="$seedfiles $1"
+		elif [ $progname = "fftns" -o  $progname = "nwns" ]; then
+			if [ "$1" -gt 0 ]; then
+				cycle=`expr "$1" - 0`
+			fi
+		else
+			echo "Unknown option:  $1" 1>&2
+			er=1;
+		fi
+		shift   
+	done;
+
+
+
+#	TMPFILE=/tmp/$progname.$$
+	TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`
+	if [ $? -ne 0 ]; then
+		echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
+		TMPFILE=`mktemp -d /tmp/$progname.XXXXXXXXXX`
+	fi	
+	umask 077
+#	mkdir  $TMPFILE  || er=1
+	if [ $debug -eq 1 ]; then
+		trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0
+	else
+		trap "rm -rf $TMPFILE " 0
+	fi
+	if [ $# -eq 1 ]; then
+		if [ -r "$1" -o "$1" = - ]; then
+
+			if [ -r "$addfile" ]; then
+				printf '';
+			else
+				echo "$0": Cannot open "$addfile". 1>&2
+				exit 1;
+			fi
+
+			cat "$1"              | tr "\r" "\n" > $TMPFILE/infile 
+			echo ""                             >> $TMPFILE/infile
+			cat "$addfile"        | tr "\r" "\n" | grep -v "^$" >> $TMPFILE/infile
+			cat "$addfile"        | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_addfile
+			cat "$aamatrix"       | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_aamtx
+			cat "$treeinfile"     | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_guidetree
+			cat "$seedtablefile"  | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_seedtablefile
+			cat "$laraparams"     | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_lara.params
+#			echo $seedfiles
+			infilename="$1"
+			seedfilesintmp="/dev/null"
+			seednseq="0"
+			set $seedfiles > /dev/null
+			while [ $# -gt 1 ];
+			do
+				shift
+				if [ -r "$1" ]; then
+					cat "$1" | tr "\r" "\n" >  $TMPFILE/seed$#
+				else
+					echo "$0": Cannot open "$1". 1>&2
+					exit 1;
+				fi
+				seednseq=$seednseq" "`grep -c '^[>|=]' $TMPFILE/seed$#`
+				seedfilesintmp=$seedfilesintmp" "seed$#
+			done
+#			ls $TMPFILE
+#			echo $seedfilesintmp
+#			echo $seednseq
+
+
+		else
+			echo "$0": Cannot open "$1". 1>&2
+			er=1
+#			exit 1;
+		fi
+	else
+		echo '$#'"=$#" 1>&2
+		er=1
+	fi
+
+
+	if [ $os != "linux" ]; then
+		numthreads=0
+	fi
+
+	if [ $numthreads -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
+		echo 'Impossible' 1>&2;
+		exit 1;
+	fi
+
+	if [ $auto -eq 1 ]; then
+		"$prefix/countlen" < $TMPFILE/infile > $TMPFILE/size
+		nseq=`awk '{print $1}' $TMPFILE/size`
+		nlen=`awk '{print $3}' $TMPFILE/size`
+		if [ $nlen -lt 2000 -a $nseq -lt 100 ]; then
+			distance="local"
+			iterate=1000
+		elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
+			distance="sixtuples"
+			iterate=2
+		else
+			distance="sixtuples"
+			iterate=0
+		fi
+		if [ $quiet -eq 0 ]; then
+			echo "nseq = " $nseq              1>&2
+			echo "nlen = " $nlen              1>&2
+			echo "distance = " $distance      1>&2
+			echo "iterate = " $iterate        1>&2
+		fi
+	fi
+
+	if [ $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 $contrafold -eq 1 ]; then
+		rnaopt=" -o $rgop -c $weightm -r $weightr "
+#		rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx "
+		rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx "
+	else
+		rnaopt="  "
+		rnaoptit=" -F "
+	fi
+
+	model="$sbstmodel $kappa $fmodel"
+
+	if [ $er -eq 1 ]; then
+		echo "------------------------------------------------------------------------------" 1>&2
+		echo "  MAFFT" $version 1>&2
+#		echo "" 1>&2
+#		echo "  Input format: fasta" 1>&2
+#		echo ""  1>&2
+#		echo "  Usage: `basename $0` [options] inputfile > outputfile" 1>&2
+	    echo "  http://mafft.cbrc.jp/alignment/software/" 1>&2
+		echo "  NAR 30:3059-3066 (2002), Briefings in Bioinformatics 9:286-298 (2008)"        1>&2
+#		echo "------------------------------------------------------------------------------" 1>&2
+#		echo "  % mafft in > out" 1>&2
+		echo "------------------------------------------------------------------------------" 1>&2
+#		echo ""  1>&2
+		echo "High speed:" 1>&2
+		echo "  % mafft in > out" 1>&2
+		echo "  % mafft --retree 1 in > out (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. (# must be <= number of physical cores - 1)" 1>&2
+#		echo "" 1>&2
+#		echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2
+#		echo " most accurate in many cases, assumes only one alignable domain" 1>&2 
+#		echo "" 1>&2
+#		echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2
+#		echo " works well if many unalignable residues exist between alignable domains" 1>&2
+#		echo "" 1>&2
+#		echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2
+#		echo " suitable for globally alignable sequences            " 1>&2
+#		echo "" 1>&2
+#		echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2
+#		echo " accurate and slow, iterative refinement method      " 1>&2
+#		echo "" 1>&2
+#		echo "If the input sequences are long (~1,000,000nt)," 1>&2
+#		echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2
+#		echo "" 1>&2
+#		echo "If many (~5,000) sequences are to be aligned," 1>&2
+#		echo "" 1>&2
+#		echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2
+#		echo "" 1>&2
+#		echo " --localpair :      All pairwise local alignment information is included"  1>&2
+#		echo "                    to the objective function, default: off"  1>&2
+#		echo " --globalpair :     All pairwise global alignment information is included"  1>&2
+#		echo "                    to the objective function, default: off"  1>&2
+#		echo " --op # :           Gap opening penalty, default: $defaultgop " 1>&2
+#		echo " --ep # :           Offset (works like gap extension penalty), default: $defaultaof " 1>&2
+#		echo " --bl #, --jtt # :  Scoring matrix, default: BLOSUM62" 1>&2
+#		echo "                    Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2
+#		echo "                    or JTT (--jtt) # PAM. " 1>&2
+#		echo " --nuc or --amino : Sequence type, default: auto" 1>&2
+#		echo " --retree # :       The number of tree building in progressive method " 1>&2
+#		echo "                    (see the paper for detail), default: $defaultcycle " 1>&2
+#		echo " --maxiterate # :   Maximum number of iterative refinement, default: $defaultiterate " 1>&2
+#		if [ $defaultfft -eq 1 ]; then
+#			echo " --fft or --nofft:  FFT is enabled or disabled, default: enabled" 1>&2
+#		else
+#			echo " --fft or --nofft:  FFT is enabled or disabled, default: disabled" 1>&2
+#		fi
+#		echo " --memsave:         Memory saving mode" 1>&2
+#		echo "                    (for long genomic sequences), default: off" 1>&2
+#		echo " --clustalout :     Output: clustal format, default: fasta" 1>&2
+#		echo " --reorder :        Outorder: aligned, default: input order" 1>&2
+#		echo " --quiet :          Do not report progress" 1>&2
+#		echo "-----------------------------------------------------------------------------" 1>&2
+		exit 1; 
+	fi
+	if [ $sw -eq 1 ]; then
+		swopt=" -A "
+	else
+		swopt=" "
+	fi
+
+	if [ $distance = "fasta" -o $partdist = "fasta" ]; then
+		if [ ! "$FASTA_4_MAFFT" ]; then
+			FASTA_4_MAFFT=`which fasta34`
+		fi
+
+		if [ ! -x "$FASTA_4_MAFFT" ]; then
+			echo ""       1>&2
+			echo "== Install FASTA ========================================================" 1>&2
+			echo "This option requires the fasta34 program (FASTA version x.xx or higher)"   1>&2
+			echo "installed in your PATH.  If you have the fasta34 program but have renamed" 1>&2
+			echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2
+			echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2
+			echo "=========================================================================" 1>&2
+			echo "" 1>&2
+			exit 1
+		fi
+	fi
+	if [ $distance = "lara" -o $distance = "slara" ]; then
+		if [ ! -x "$prefix/mafft_lara" ]; then
+			echo ""       1>&2
+			echo "== Install LaRA =========================================================" 1>&2
+			echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)."     1>&2
+			echo "The executable have to be renamed to 'mafft_lara' and installed into "     1>&2
+			echo "the $prefix directory. "                                                   1>&2
+			echo "A configuration file of LaRA also have to be given"                        1>&2
+			echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
+			echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
+			echo "=========================================================================" 1>&2
+			echo "" 1>&2
+			exit 1
+		fi
+		if [ ! -s "$laraparams" ]; then
+			echo ""       1>&2
+			echo "== Configure LaRA =======================================================" 1>&2
+			echo "A configuration file of LaRA have to be given"                             1>&2
+			echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
+			echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
+			echo "=========================================================================" 1>&2
+			echo "" 1>&2
+			exit 1
+		fi
+	fi
+	if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
+	if [ ! -x "$prefix/foldalign210" ]; then
+			echo ""       1>&2
+			echo "== Install FOLDALIGN ====================================================" 1>&2
+			echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2
+			echo "The executable have to be renamed to 'foldalign210' and installed into "   1>&2
+			echo "the $prefix directory. "                                                   1>&2
+			echo "=========================================================================" 1>&2
+			echo "" 1>&2
+			exit 1
+		fi
+	fi
+	if [ $distance = "scarna" ]; then
+		if [ ! -x "$prefix/mxscarnamod" ]; then
+			echo ""       1>&2
+			echo "== Install MXSCARNA ======================================================" 1>&2
+			echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required."          1>&2
+			echo "Please 'make' at the 'extensions' directory of the MAFFT source package,"   1>&2
+			echo "which contains the modified version of MXSCARNA."                           1>&2
+			echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html "                1>&2
+			echo "==========================================================================" 1>&2
+			echo "" 1>&2
+			exit 1
+		fi
+	fi
+	if [ $mccaskill -eq 1 ]; then
+		if [ ! -x "$prefix/mxscarnamod" ]; then
+			echo ""       1>&2
+			echo "== Install MXSCARNA ======================================================" 1>&2
+			echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required."          1>&2
+			echo "Please 'make' at the 'extensions' directory of the MAFFT source package,"   1>&2
+			echo "which contains the modified version of MXSCARNA."                           1>&2
+			echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html "                1>&2
+			echo "==========================================================================" 1>&2
+			echo "" 1>&2
+			exit 1
+		fi
+	fi
+	if [ $contrafold -eq 1 ]; then
+		if [ ! -x "$prefix/contrafold" ]; then
+			echo ""       1>&2
+			echo "== Install CONTRAfold ===================================================" 1>&2
+			echo "This option requires CONTRAfold"                                           1>&2
+			echo "(Do et al. http://contra.stanford.edu/contrafold/)."                       1>&2
+			echo "The executable 'contrafold' have to be installed into "                    1>&2
+			echo "the $prefix directory. "                                                   1>&2
+			echo "=========================================================================" 1>&2
+			echo "" 1>&2
+			exit 1
+		fi
+	fi
+
+#old
+#	if [ $treeout -eq 1 ]; then
+#		parttreeoutopt="-t"
+#		if [ $cycle -eq 0 ]; then
+#			treeoutopt="-t -T"
+#			groupsize=1
+#			iterate=0 
+#			if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+#				distance="distonly"
+#			fi
+#		else
+#			treeoutopt="-t"
+#		fi
+#	else
+#		parttreeoutopt=" "
+#		if [ $cycle -eq 0 ]; then
+#			treeoutopt="-t -T"
+#			iterate=0 
+#			if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+#				distance="distonly"
+#			fi
+#		else
+#			treeoutopt=" "
+#		fi
+#	fi
+
+#new
+	if [ $cycle -eq 0 ]; then
+		treeoutopt="-t -T"
+		iterate=0 
+		if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+			distance="distonly"
+		fi
+		if [ $treeout -eq 1 ]; then
+			parttreeoutopt="-t"
+			groupsize=1
+		else
+			parttreeoutopt=" "
+		fi
+		if [ $distout -eq 1 ]; then
+			distoutopt="-y -T"
+		fi
+	else
+		if [ $treeout -eq 1 ]; then
+			parttreeoutopt="-t"
+			treeoutopt="-t"
+		else
+			parttreeoutopt=" "
+			treeoutopt=" "
+		fi
+		if [ $distout -eq 1 ]; then
+			distoutopt="-y"
+		fi
+	fi
+#
+
+	formatcheck=`grep -c '^[[:blank:]]\+>' $TMPFILE/infile | head -1 `
+	if [ $formatcheck -gt 0 ]; then
+		echo "The first character of a description line must be " 1>&2
+		echo "the greater-than (>) symbol, not a blank."           1>&2
+		echo "Please check the format around the following line(s):"  1>&2
+		grep -n '^[[:blank:]]\+>' $TMPFILE/infile  1>&2
+		exit 1
+	fi
+
+	nseq=`grep -c '^[>|=]' $TMPFILE/infile | head -1 ` 
+	if [ $nseq -eq 2 ]; then
+		cycle=1
+	fi
+	if [ $cycle -gt 3 ]; then
+		cycle=3
+	fi
+
+	if [ $nseq -gt 4000 -a $iterate -gt 1 ]; then
+		echo "Too many sequences to perform iterative refinement!" 1>&2
+		echo "Please use a progressive method." 1>&2
+		exit 1
+	fi
+
+
+	if [ $distance = "sixtuples" -a \( $seed = "x" -a $seedtable = "x" \) ]; then
+		localparam=" "
+	elif [ $distance = "sixtuples" -a \( $seed != "x" -o $seedtable != "x" \) ]; then
+		if [ $cycle -lt 2 ]; then
+			cycle=2                # nazeda
+		fi
+		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=" "
+		if [ $groupsize -gt -1 ]; then
+			cycle=1
+		fi
+	else
+		localparam=" -l "$weighti
+		if [ $cycle -gt 1 ]; then  # 09/01/08
+			cycle=1
+		fi
+	fi
+
+	if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
+		aof="0.000"
+	fi
+
+	if [ "$memopt" = " -M -B " -a "$distance" != "sixtuples" ]; then
+		echo "Impossible" 1>&2
+		exit 1
+	fi
+#exit
+
+	if [ $distance = "parttree" ]; then
+		if [ $seed != "x" -o $seedtable != "x" ]; then
+			echo "Impossible" 1>&2
+			exit 1
+		fi
+		if [ $iterate -gt 1 ]; then
+			echo "Impossible" 1>&2
+			exit 1
+		fi
+		if [ $outorder = "aligned" ]; then
+			outorder="input"
+		fi
+		outorder="input"   # partorder ga kiku
+		if [ $partdist = "localalign" ]; then
+			splitopt=" -L "    # -L -l -> fast 
+		elif [ $partdist = "fasta" ]; then
+			splitopt=" -S "
+		else
+			splitopt="  "
+		fi
+	fi
+
+
+#	if [ $nseq -gt 5000 ]; then
+#		fft=0
+#	fi
+	if [ $forcefft -eq 1 ]; then
+		param_fft=" -G "
+		fft=1
+	elif [ $fft -eq 1 ]; then
+		param_fft=" -F "
+	else
+		param_fft=" "
+	fi
+
+	if [ $seed != "x" -a $seedtable != "x" ]; then
+			echo 'Use either one of seedtable and seed.  Not both.' 1>&2
+			exit 1
+	fi
+#	if [ $seedtable != "x" -a $anysymbol -gt 0 ]; then
+#			echo 'The combination of --seedtable and --anysymbol is not supported.' 1>&2
+#			exit 1
+#	fi
+
+	if [ $treein -eq 1 ]; then
+#		if [ $iterate -gt 0 ]; then
+#			echo 'Not supported yet.' 1>&2
+#			exit 1
+#		fi
+		cycle=1
+	fi
+
+	if [ "$addarg0" != " " ]; then
+		"$prefix/countlen" < $TMPFILE/_addfile > $TMPFILE/addsize
+		nadd=`awk '{print $1}' $TMPFILE/addsize`
+		if [ $nadd -eq "0" ]; then
+			echo Check $addfile 1>&2
+			exit 1;
+		fi
+		addarg="$addarg0 $nadd"
+		cycle=1
+		iterate=0
+		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
+	fi
+
+	if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+		if [ $distance = "sixtuples" ]; then
+			echo 'Not supported.' 1>&2
+			echo 'Please add --globalpair, --localpair, --scarnapair,' 1>&2
+			echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
+			exit 1
+		fi
+	fi
+
+	if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
+		if [ $distance = "scarna" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
+			strategy="X-I"
+		elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
+			strategy="Q-I"
+		fi
+	elif [ $distance = "fasta" -a $sw -eq 0 ]; then
+		strategy="F-I"
+	elif [ $distance = "fasta" -a $sw -eq 1 ]; then
+		strategy="H-I"
+	elif [ $distance = "blast" ]; then
+		strategy="B-I"
+	elif [ $distance = "global" -o $distance = "distonly" ]; then
+		strategy="G-I"
+	elif [ $distance = "local" ]; then
+		strategy="L-I"
+	elif [ $distance = "localgenaf" ]; then
+		strategy="E-I"
+	elif [ $distance = "globalgenaf" ]; then
+		strategy="K-I"
+	elif [ $fft -eq 1 ]; then
+		strategy="FFT-"
+	else
+		strategy="NW-"
+	fi
+	strategy=$strategy"NS-"
+	if [ $iterate -gt 0 ]; then
+		strategy=$strategy"i"
+	elif [ $distance = "parttree" ]; then
+		if [ $partdist = "fasta" ]; then
+			strategy=$strategy"FastaPartTree-"$cycle
+		elif [ $partdist = "localalign" ]; then
+			strategy=$strategy"DPPartTree-"$cycle
+		else
+			strategy=$strategy"PartTree-"$cycle
+		fi
+	else
+		strategy=$strategy$cycle
+	fi
+
+	explanation='?'
+	performance='Not tested.'
+	if [ $strategy = "F-INS-i" ]; then
+		explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
+		performance='Most accurate, but very slow'
+	elif [ $strategy = "L-INS-i" ]; then
+		explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
+		performance='Probably most accurate, very slow'
+	elif [ $strategy = "E-INS-i" ]; then
+		explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)'
+		performance='Suitable for sequences with long unalignable regions, very slow'
+	elif [ $strategy = "G-INS-i" ]; then
+		explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information'
+		performance='Suitable for sequences of similar lengths, very slow'
+	elif [ $strategy = "X-INS-i" ]; then
+		explanation='RNA secondary structure information is taken into account.'
+		performance='For short RNA sequences only, extremely slow'
+	elif [ $strategy = "F-INS-1" ]; then
+		explanation='Progressive method incorporating LOCAL pairwise alignment information'
+	elif [ $strategy = "L-INS-1" ]; then
+		explanation='Progressive method incorporating LOCAL pairwise alignment information'
+	elif [ $strategy = "G-INS-1" ]; then
+		explanation='Progressive method incorporating GLOBAL pairwise alignment information'
+	elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then
+		explanation='Iterative refinement method (max. '$iterate' iterations)'
+		if [ $iterate -gt 2 ]; then
+			performance='Accurate but slow'
+		else
+			performance='Standard'
+		fi
+	elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then
+		explanation='Progressive method (guide trees were built '$cycle' times.)'
+		performance='Fast but rough'
+	elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then
+		explanation='Progressive method (rough guide tree was used.)'
+		performance='Very fast but very rough'
+	fi
+
+	if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
+		outputopt=" -c $strategy -r $TMPFILE/order  "
+	elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
+		outputopt=" -c $strategy  "
+	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 -r $TMPFILE/order "
+	else
+		outputopt="null"
+	fi
+	
+	(
+		cd $TMPFILE;
+
+		if [ $quiet -gt 0 ]; then
+
+			if [ $anysymbol -eq 1 ]; then
+				mv infile orig
+				"$prefix/replaceu" -i orig > infile 2>/dev/null || exit 1
+			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 > /dev/null
+#				echo $#
+				while [ $# -gt 1 ]
+				do
+					shift
+#					echo "num="$#
+
+					if [ $anysymbol -eq 1 ]; then
+						cat seed$# >> orig
+						"$prefix/replaceu" -i seed$# -o $seedoffset > clean 2>/dev/null || exit 1
+						mv clean seed$#
+					fi
+					"$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>/dev/null || exit 1
+					cat hat3 >> hat3.seed
+#					echo "$1"
+					seedoffset=`expr $seedoffset + $1`
+#					echo "$1"
+#					echo "seedoffset="$seedoffset
+				done;
+#				echo "seedoffset="$seedoffset
+				if [ $anysymbol -eq 1 ]; then
+					"$prefix/replaceu" -i orig2 -o $seedoffset >> infile 2>/dev/null || exit 1  # yarinaoshi
+					cat orig2 >> orig
+				else
+					cat infile2 >> infile
+				fi
+			elif [ $seedtable != "x" ]; then
+				cat _seedtablefile > hat3.seed
+			else
+				cat /dev/null > hat3.seed
+			fi
+#			cat hat3.seed
+
+
+			if [ $mccaskill -eq 1 ]; then
+				"$prefix/mccaskillwrap" -C $numthreads -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
+			elif [ $contrafold -eq 1 ]; then
+				"$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
+			fi
+			if [ $distance = "fasta" ]; then
+				"$prefix/dndfast7" $swopt < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "blast" ]; then
+				"$prefix/dndblast" < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "foldalignlocal" ]; then
+				"$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "foldalignglobal" ]; then
+				"$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "slara" ]; then
+				"$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "lara" ]; then
+				"$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "scarna" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "global" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -F < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "local" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $lexp -f $lgop  -h $laof -L < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "globalgenaf" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null 2>&1    || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "localgenaf" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null  2>&1      || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "distonly" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null  2>&1      || exit 1
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "parttree" ]; then
+				"$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre 2>/dev/null || exit 1
+				mv hat3.seed hat3
+			else
+				"$prefix/disttbfast" -O $outnum $addarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $algopt $treealg $scoreoutarg < infile   > pre 2>/dev/null || exit 1
+				mv hat3.seed hat3
+			fi
+			while [ $cycle -gt 1 ]
+			do
+				if [ $distance = "parttree" ]; then
+					mv pre infile
+					"$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre 2>/dev/null || exit 1
+				else
+					"$prefix/tbfast" -O $outnum -C $numthreads $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model  -f "-"$gop  -h "-"$aof $param_fft  $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>&1 || exit 1
+				fi
+				cycle=`expr $cycle - 1`
+			done
+			if [ $iterate -gt 0 ]; then
+				if [ $distance = "sixtuples" ]; then
+				    "$prefix/dndpre" -C $numthreads < pre     > /dev/null 2>&1 || exit 1
+				fi
+				"$prefix/dvtditr" -C $numthreads -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof  -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy  $scoreoutarg < pre     > /dev/null 2>&1 || exit 1
+			fi
+		else
+
+			if [ $anysymbol -eq 1 ]; then
+				mv infile orig
+				"$prefix/replaceu" -i orig > infile || exit 1
+			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 > /dev/null
+#				echo $#
+				while [ $# -gt 1 ]
+				do
+					shift
+#					echo "num="$#
+
+					if [ $anysymbol -eq 1 ]; then
+						cat seed$# >> orig
+						"$prefix/replaceu" -i seed$# -o $seedoffset > clean || exit 1
+						mv clean seed$#
+					fi
+					"$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile || exit 1
+					cat hat3 >> hat3.seed
+#					echo "$1"
+					seedoffset=`expr $seedoffset + $1`
+#					echo "$1"
+#					echo "seedoffset="$seedoffset
+				done;
+#				echo "seedoffset="$seedoffset
+				if [ $anysymbol -eq 1 ]; then
+					"$prefix/replaceu" -i orig2 -o $seedoffset >> infile || exit 1 # yarinaoshi
+					cat orig2 >> orig
+				else
+					cat infile2 >> infile
+				fi
+			elif [ $seedtable != "x" ]; then
+				cat _seedtablefile > hat3.seed
+			else
+				cat /dev/null > hat3.seed
+			fi
+#			cat hat3.seed
+
+			if [ $mccaskill -eq 1 ]; then
+				"$prefix/mccaskillwrap" -C $numthreads -d "$prefix" -i infile > hat4  || exit 1
+			elif [ $contrafold -eq 1 ]; then
+				"$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4  || exit 1
+			fi
+			if [ $distance = "fasta" ]; then
+				"$prefix/dndfast7" $swopt < infile > /dev/null     || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg $scoreoutarg < infile   > /dev/null || exit 1
+			elif [ $distance = "blast" ]; then
+				"$prefix/dndblast" < infile > /dev/null     || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg $scoreoutarg < infile   > /dev/null || exit 1
+			elif [ $distance = "foldalignlocal" ]; then
+				"$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "foldalignglobal" ]; then
+				"$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop  -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "slara" ]; then
+				"$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "lara" ]; then
+				"$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "scarna" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null   || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>&1 || exit 1
+			elif [ $distance = "global" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof   -F  < infile > /dev/null     || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg $scoreoutarg < infile   > /dev/null || exit 1
+			elif [ $distance = "local" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $lexp -f $lgop  -h $laof -L  < infile > /dev/null     || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg $scoreoutarg < infile   > /dev/null || exit 1
+			elif [ $distance = "globalgenaf" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null     || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg $scoreoutarg < infile   > /dev/null || exit 1
+			elif [ $distance = "localgenaf" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N  < infile > /dev/null     || exit 1
+				cat hat3.seed hat3 > hatx
+				mv hatx hat3
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg $scoreoutarg < infile   > /dev/null || exit 1
+			elif [ $distance = "distonly" ]; then
+				"$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null            || exit 1
+				"$prefix/tbfast" $outnum $addarg -C $numthreads $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg $scoreoutarg < infile   > /dev/null || exit 1
+			elif [ $distance = "parttree" ]; then
+				"$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre || exit 1
+				mv hat3.seed hat3
+			else
+				"$prefix/disttbfast" -O $outnum $addarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft  $algopt $treealg $scoreoutarg < infile   > pre || exit 1
+				mv hat3.seed hat3
+			fi
+
+			while [ $cycle -gt 1 ]
+			do
+				if [ $distance = "parttree" ]; then
+					mv pre infile
+					"$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile  > pre || exit 1
+				else
+					"$prefix/tbfast" -O $outnum -C $numthreads $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model  -f "-"$gop  -h "-"$aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null || exit 1
+				fi
+				cycle=`expr $cycle - 1`
+			done
+			if [ $iterate -gt 0 ]; then
+				if [ $distance = "sixtuples" ]; then
+			    	"$prefix/dndpre" -C $numthreads < pre     > /dev/null 2>&1 || exit 1
+				fi
+				"$prefix/dvtditr" -C $numthreads -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy  $scoreoutarg < pre     > /dev/null || exit 1
+			fi
+		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" -a pre -i orig > restored || exit 1
+			mv restored pre
+		fi
+
+		if [ $quiet -eq 0 ]; then
+			echo '' 1>&2
+			if [ $mccaskill -eq 1 ]; then
+				echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>&2
+				echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>&2
+				echo "incorporated in the iterative alignment process (4)." 1>&2
+				echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>&2
+				echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>&2
+				echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>&2
+				echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
+				echo "" 1>&2
+			elif [ $contrafold -eq 1 ]; then
+				echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>&2
+				echo "and then incorporated in the iterative alignment process (4)." 1>&2
+				echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>&2
+				echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
+				echo "" 1>&2
+			fi
+			if [ $distance = "fasta" -o $partdist = "fasta" ]; then
+				echo "Pairwise alignments were computed by FASTA" 1>&2
+				echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>&2
+			fi
+			if [ $distance = "blast" ]; then
+				echo "Pairwise alignments were computed by BLAST" 1>&2
+				echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>&2
+			fi
+			if [ $distance = "scarna" ]; then
+				echo "Pairwise alignments were computed by MXSCARNA" 1>&2
+				echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>&2
+			fi
+			if [ $distance = "lara" -o $distance = "slara" ]; then
+				echo "Pairwise alignments were computed by LaRA" 1>&2
+				echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>&2
+			fi
+			if [ $distance = "foldalignlocal" ]; then
+				echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>&2
+				echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
+			fi
+			if [ $distance = "foldalignglobal" ]; then
+				echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>&2
+				echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
+			fi
+			printf "\n" 1>&2
+			echo 'Strategy:' 1>&2
+			printf ' '$strategy 1>&2
+			echo ' ('$performance')' 1>&2
+			echo ' '$explanation 1>&2
+			echo '' 1>&2
+			echo "If unsure which option to use, try 'mafft --auto input > output'." 1>&2
+#			echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>&2
+			echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>&2
+			echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>&2
+			echo '' 1>&2
+		fi
+	)
+
+	if [ "$outputfile" = "" ]; then
+		if [ "$outputopt" = "null" ]; then
+			cat < $TMPFILE/pre || exit 1
+		else
+			"$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre || exit 1
+		fi
+	else
+		if [ "$outputopt" = "null" ]; then
+			cat < $TMPFILE/pre > "$outputfile" || exit 1
+		else
+			"$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre > "$outputfile" || exit 1
+		fi
+	fi
+
+	if [ $treeout -eq 1 ]; then
+		cp $TMPFILE/infile.tree "$infilename.tree"
+	fi
+
+	if [ $distout -eq 1 ]; then
+		cp $TMPFILE/hat2 "$infilename.hat2"
+	fi
+
+	exit 0;
+fi
+
+prog="awk"
+
+tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
+if [ -x "$tmpawk" ]; then
+	prog="$tmpawk"
+fi
+
+tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
+if [ -x "$tmpawk" ]; then
+	prog="$tmpawk"
+fi
+
+#echo "prog="$prog 1>&2
+
+umask 077
+(
+$prog '
+BEGIN {
+	prefix = ENVIRON["prefix"];
+	version = ENVIRON["version"];
+	myself = ENVIRON["myself"];
+	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) 2011 Kazutaka Katoh\n" )                                  > "/dev/tty";
+		printf( "        NAR 30:3059-3066, NAR 33:511-518\n" )                                   > "/dev/tty";
+		printf( "        http://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)\n@ " ) > "/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( "OK?\n" ) > "/dev/tty";
+			printf( "@ [Y] " ) > "/dev/tty";
+			res = getline < "/dev/tty";
+			close( "/dev/tty" );
+			if( res == 0 )
+				continue;
+			else if( NF == 0 || $0 ~ /^[Yy]/ )
+			{
+				go=1;
+				break;
+			}
+			else
+				break;
+		}
+		if( go ) break;
+		printf( "\n" ) > "/dev/tty";
+		printf( "\n" ) > "/dev/tty";
+	}
+	system( command );
+	command = sprintf( "less \"%s\"", outfile );
+	system( command );
+	printf( "Press Enter to exit." ) > "/dev/tty";
+	res = getline < "/dev/tty";
+}
+'
+)
+exit 0;
diff --git a/binaries/linuxAMD64/mafft/mafft-distance b/binaries/linuxAMD64/mafft/mafft-distance
index 59add95..b4f35d7 100644
Binary files a/binaries/linuxAMD64/mafft/mafft-distance and b/binaries/linuxAMD64/mafft/mafft-distance differ
diff --git a/binaries/linuxAMD64/mafft/mafft-homologs.rb b/binaries/linuxAMD64/mafft/mafft-homologs.rb
new file mode 100644
index 0000000..c1a2468
--- /dev/null
+++ b/binaries/linuxAMD64/mafft/mafft-homologs.rb
@@ -0,0 +1,374 @@
+#!/usr/bin/env ruby
+
+localdb = "sp"        
+# database name from which homologues are collected 
+# by locally installed blast. Leave this if you do 
+# not use the '-l' option.
+
+mafftpath = "/usr/bin/mafft"   
+# path of mafft. "/usr/local/bin/mafft"
+# if mafft is in your command path, "mafft" is ok.
+
+blastpath = "blastall"   
+# path of blastall. 
+# if blastall is in your command path, "blastall" is ok.
+
+# mafft-homologs.rb  v. 2.1 aligns sequences together with homologues 
+# automatically collected from SwissProt via NCBI BLAST.
+#
+# mafft > 5.58 is required
+#
+# Usage:
+#   mafft-homologs.rb [options] input > output
+# Options:
+#   -a #      the number of collected sequences (default: 50)
+#   -e #      threshold value (default: 1e-10)
+#   -o "xxx"  options for mafft 
+#             (default: " --op 1.53 --ep 0.123 --maxiterate 1000")
+#   -l        locally carries out blast searches instead of NCBI blast
+#             (requires locally installed blast and a database)
+#   -f        outputs collected homologues also (default: off)
+#   -w        entire sequences are subjected to BLAST search 
+#             (default: well-aligned region only)
+
+require 'getopts'
+require 'tempfile'
+
+# mktemp
+GC.disable
+temp_vf = Tempfile.new("_vf").path
+temp_if = Tempfile.new("_if").path
+temp_pf = Tempfile.new("_pf").path
+temp_af = Tempfile.new("_af").path
+temp_qf = Tempfile.new("_qf").path
+temp_bf = Tempfile.new("_bf").path
+temp_rid = Tempfile.new("_rid").path
+temp_res = Tempfile.new("_res").path
+
+
+system( mafftpath + " --help > #{temp_vf} 2>&1" )
+pfp = File.open( "#{temp_vf}", 'r' )
+while pfp.gets
+	break if $_ =~ /MAFFT v/
+end
+pfp.close
+if( $_ ) then
+	mafftversion = sub( /^\D*/, "" ).split(" ").slice(0).strip.to_s
+else
+	mafftversion = "0"
+end
+if( mafftversion < "5.58" ) then
+	puts ""
+	puts "======================================================"
+	puts "Install new mafft (v. >= 5.58)"
+	puts "======================================================"
+	puts ""
+	exit
+end
+
+srand ( 0 )
+
+def readfasta( fp, name, seq )
+	nseq = 0
+	tmpseq = ""
+	while fp.gets
+		if $_ =~ /^>/ then
+			name.push( $_.sub(/>/,"").strip )
+			seq.push( tmpseq ) if nseq > 0
+			nseq += 1
+			tmpseq = ""
+		else
+			tmpseq += $_.strip
+		end
+	end
+	seq.push( tmpseq )
+	return nseq
+end
+
+nadd = 50
+eval = 1e-10
+local = 0
+fullout = 0
+entiresearch = 0
+corewin = 50
+corethr = 0.3
+mafftopt = " --op 1.53 --ep 0.123 --localpair --maxiterate 1000 --reorder "
+if getopts( "s", "f", "w", "l", "h", "e:", "a:", "o:", "c:", "d:" ) == nil ||  ARGV.length == 0 || $OPT_h then
+	puts "Usage: #{$0} [-h -l -e# -a# -o\"[options for mafft]\"] input_file"
+	exit
+end
+
+if $OPT_c then
+	corewin = $OPT_c.to_i
+end
+if $OPT_d then
+	corethr = $OPT_d.to_f
+end
+if $OPT_w
+	entiresearch = 1
+end
+if $OPT_f
+	fullout = 1
+end
+if $OPT_s
+	fullout = 0
+end
+if $OPT_l
+	local = 1
+end
+if $OPT_e then
+	eval = $OPT_e.to_f
+end
+if $OPT_a then
+	nadd = $OPT_a.to_i
+end
+if $OPT_o then
+	mafftopt += " " + $OPT_o + " "
+end
+
+system "cat " + ARGV.to_s + " > #{temp_if}"
+ar = mafftopt.split(" ")
+nar = ar.length
+for i in 0..(nar-1)
+	if ar[i] == "--seed" then
+		system "cat #{ar[i+1]} >> #{temp_if}"
+	end
+end
+
+nseq = 0
+ifp = File.open( "#{temp_if}", 'r' )
+	while ifp.gets
+		nseq += 1 if $_ =~ /^>/
+	end
+ifp.close
+
+if nseq >= 100 then
+	STDERR.puts "The number of input sequences must be <100."
+	exit
+elsif nseq == 1 then
+	system( "cp #{temp_if}"  + " #{temp_pf}" )
+else
+	STDERR.puts "Performing preliminary alignment .. "
+	if entiresearch == 1 then
+#		system( mafftpath + " --maxiterate 1000 --localpair #{temp_if} > #{temp_pf}" )
+		system( mafftpath + " --maxiterate 0 --retree 2 #{temp_if} > #{temp_pf}" )
+	else
+		system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} #{temp_if} > #{temp_pf}" )
+	end
+end
+
+pfp = File.open( "#{temp_pf}", 'r' )
+inname = []
+inseq = []
+slen = []
+act = []
+nin = 0
+nin = readfasta( pfp, inname, inseq )
+for i in 0..(nin-1)
+	slen.push( inseq[i].gsub(/-/,"").length )
+	act.push( 1 )
+end
+pfp.close
+
+pfp = File.open( "#{temp_if}", 'r' )
+orname = []
+orseq = []
+nin = 0
+nin = readfasta( pfp, orname, orseq )
+pfp.close
+
+allen = inseq[0].length
+for i in 0..(nin-2)
+	for j in (i+1)..(nin-1)
+		next if act[i] == 0
+		next if act[j] == 0
+		pid = 0.0
+		total = 0
+		for a in 0..(allen-1)
+			next if inseq[i][a,1] == "-" || inseq[j][a,1] == "-"
+			total += 1
+			pid += 1.0 if inseq[i][a,1] == inseq[j][a,1]
+		end
+		pid /= total
+#		puts "#{i.to_s}, #{j.to_s}, #{pid.to_s}"
+		if pid > 0.5 then
+			if slen[i] < slen[j]
+				act[i] = 0 
+			else
+				act[j] = 0 
+			end
+		end
+	end
+end
+#p act
+
+
+afp = File.open( "#{temp_af}", 'w' )
+
+STDERR.puts "Searching .. \n"
+ids = []
+add = []
+sco = []
+for i in 0..(nin-1)
+	inseq[i].gsub!(/-/,"")
+	afp.puts ">" + orname[i]
+	afp.puts orseq[i]
+
+#	afp.puts ">" + inname[i]
+#	afp.puts inseq[i]
+
+	STDERR.puts "Query (#{i+1}/#{nin})\n" + inname[i]
+	if act[i] == 0 then
+		STDERR.puts "Skip.\n\n"
+		next 
+	end
+
+	if local == 0 then
+		command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > #{temp_rid}"
+		system command
+	
+		ridp = File.open( "#{temp_rid}", 'r' )
+		while ridp.gets
+			break if $_ =~ / RID = (.*)/
+		end
+		ridp.close
+		rid = $1.strip
+		STDERR.puts "Submitted to NCBI. rid = " + rid
+	
+		STDERR.printf "Waiting "
+		while 1 
+			STDERR.printf "."
+			sleep 10
+			command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > #{temp_res}"
+			system command
+			resp = File.open( "#{temp_res}", 'r' )
+#			resp.gets
+#			if $_ =~ /WAITING/ then
+#				resp.close
+#				next
+#			end
+			while( resp.gets )
+				break if $_ =~ /QBlastInfoBegin/
+			end
+			resp.gets
+			if $_ =~ /WAITING/ then
+				resp.close
+				next
+			else
+				resp.close
+				break
+			end
+		end
+	else
+#		puts "Not supported"
+#		exit
+		qfp = File.open( "#{temp_qf}", 'w' )
+			qfp.puts "> "
+			qfp.puts inseq[i]
+		qfp.close
+		command = blastpath + "  -p blastp  -e #{eval} -b 1000 -m 7 -i #{temp_qf} -d #{localdb} > #{temp_res}"
+		system command
+		resp = File.open( "#{temp_res}", 'r' )
+	end
+	STDERR.puts " Done.\n\n"
+
+	resp = File.open( "#{temp_res}", 'r' )
+	while 1
+		while resp.gets
+			break if $_ =~ /<Hit_id>(.*)<\/Hit_id>/ || $_ =~ /(<Iteration_stat>)/
+		end
+		id = $1
+		break if $_ =~ /<Iteration_stat>/
+#		p id
+		while resp.gets
+			break if $_ =~ /<Hsp_bit-score>(.*)<\/Hsp_bit-score>/
+		end
+		score = $1.to_f
+#		p score
+
+		known = ids.index( id )
+		if known != nil then
+			if sco[known] >= score then
+				next
+			else
+				ids.delete_at( known )
+				add.delete_at( known )
+				sco.delete_at( known )
+			end
+		end
+		while resp.gets
+			break if $_ =~ /<Hsp_hseq>(.*)<\/Hsp_hseq>/
+		end
+#		break if $1 == nil
+		target = $1.sub( /-/, "" ).sub( /U/, "X" )
+#		p target
+#		STDERR.puts "adding 1 seq"
+		ids.push( id )
+		sco.push( score )
+		add.push( target )
+	end
+	resp.close
+end
+
+n = ids.length
+
+outnum = 0
+while n > 0 && outnum < nadd
+	m = rand( n )
+	afp.puts ">_addedbymaffte_" + ids[m]
+	afp.puts add[m]
+	ids.delete_at( m )
+	add.delete_at( m )
+	n -= 1
+	outnum += 1
+end
+afp.close
+
+STDERR.puts "Performing alignment .. "
+system( mafftpath + mafftopt + " #{temp_af} > #{temp_bf}" )
+STDERR.puts "done."
+
+bfp = File.open( "#{temp_bf}", 'r' )
+outseq = []
+outnam = []
+readfasta( bfp, outnam, outseq )
+bfp.close
+
+outseq2 = []
+outnam2 = []
+
+len = outseq.length
+for i in 0..(len-1)
+#	p outnam[i]
+	if fullout == 0 && outnam[i] =~ /_addedbymaffte_/ then
+		next
+	end
+	outseq2.push( outseq[i] )
+	outnam2.push( outnam[i].sub( /_addedbymaffte_/, "_ho_" ) )
+end
+
+nout = outseq2.length
+len = outseq[0].length
+p = len
+while p>0
+	p -= 1
+    allgap = 1
+    for j in 0..(nout-1)
+		if outseq2[j][p,1] != "-" then
+			allgap = 0
+			break
+		end
+    end
+    if allgap == 1 then
+        for j in 0..(nout-1)
+            outseq2[j][p,1] = ""
+        end
+    end
+end
+for i in 0..(nout-1)
+	puts ">" + outnam2[i]
+	puts outseq2[i].gsub( /.{1,60}/, "\\0\n" )
+end
+
+
+system( "rm -rf #{temp_if} #{temp_vf} #{temp_af} #{temp_bf} #{temp_pf} #{temp_qf} #{temp_res} #{temp_rid}" )
diff --git a/binaries/linuxAMD64/mafft/mafft-profile b/binaries/linuxAMD64/mafft/mafft-profile
index ddf711a..06f69b1 100644
Binary files a/binaries/linuxAMD64/mafft/mafft-profile and b/binaries/linuxAMD64/mafft/mafft-profile differ
diff --git a/binaries/linuxAMD64/mafft/mafft.1 b/binaries/linuxAMD64/mafft/mafft.1
index 87ac748..8636334 100644
--- a/binaries/linuxAMD64/mafft/mafft.1
+++ b/binaries/linuxAMD64/mafft/mafft.1
@@ -1,5 +1,5 @@
 .\"     Title: MAFFT
-.\"    Author: Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
+.\"    Author: Kazutaka Katoh <kazutaka.katoh@aist.go.jp>
 .\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
 .\"      Date: 2007-08-14
 .\"    Manual: Mafft Manual
@@ -10,8 +10,13 @@
 .nh
 .\" disable justification (adjust text to left margin only)
 .ad l
+.SH "THIS MANUAL IS FOR V6.2XX (2007)"
+Recent versions (v6.8xx; 2010 Nov.) have more features than those described below.
+See also the tips page at 
+http://mafft.cbrc.jp/alignment/software/tips0.html
 .SH "NAME"
 .RS 0
+.sp
 mafft \- Multiple alignment program for amino acid or nucleotide sequences
 .RE
 .SH "SYNOPSIS"
@@ -198,7 +203,7 @@ FASTA is required.  Default: off (6mer distance is used)
 \fB\-\-weighti\fR \fInumber\fR
 .RS 4
 Weighting factor for the consistency term calculated from pairwise alignments.  Valid when 
-either of \-\-blobalpair, \-\-localpair,  \-\-genafpair, \-\-fastapair or 
+either of \-\-globalpair, \-\-localpair,  \-\-genafpair, \-\-fastapair or 
 \-\-blastpair is selected.  Default: 2.7
 .RE
 .PP
@@ -273,7 +278,7 @@ Gap opening penalty at group\-to\-group alignment.  Default: 1.53
 \fB\-\-ep\fR \fInumber\fR
 .RS 4
 Offset value, which works like gap extension penalty, for
-group\-to\-group alignment.  Deafult: 0.123
+group\-to\-group alignment.  Default: 0.123
 .RE
 .PP
 \fB\-\-lop\fR \fInumber\fR
@@ -331,7 +336,7 @@ the same to that of BLAST.  Ignored when nucleotide sequences are input.   Defau
 \fB\-\-fmodel\fR
 .RS 4
 Incorporate the AA/nuc composition information into
-the scoring matrix.  Deafult: off
+the scoring matrix.  Default: off
 .RE
 .RE
 .SS "Output"
@@ -367,12 +372,12 @@ Do not report progress.  Default: off
 .PP
 \fB\-\-nuc\fR
 .RS 4
-Assume the sequences are nucleotide.  Deafult: auto
+Assume the sequences are nucleotide.  Default: auto
 .RE
 .PP
 \fB\-\-amino\fR
 .RS 4
-Assume the sequences are amino acid.  Deafult: auto
+Assume the sequences are amino acid.  Default: auto
 .RE
 .PP
 \fB\-\-seed\fR \fIalignment1\fR [\fB--seed\fR \fIalignment2\fR \fB--seed\fR \fIalignment3\fR ...]
@@ -436,7 +441,7 @@ This variable can be set to indicate to mafft the location to the fasta34 progra
 .SH "AUTHORS"
 .RS 0
 .PP
-\fBKazutaka Katoh\fR <\&katoh_at_bioreg.kyushu\-u.ac.jp\&>
+\fBKazutaka Katoh\fR <\&kazutaka.katoh_at_aist.go.jp\&>
 .sp -1n
 .IP "" 4
 Wrote Mafft.
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