X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fbinaries%2Fmafft;h=16b666019ede41ddeb2b66acda671b2cc276bd4e;hb=8ce6db56df6c0a1c2baca2fc2d33bcb10067c6cd;hp=93578e733e5463596d304fdff0ecfa6fffea136d;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/binaries/src/mafft/binaries/mafft b/binaries/src/mafft/binaries/mafft
index 93578e7..16b6660 100644
--- a/binaries/src/mafft/binaries/mafft
+++ b/binaries/src/mafft/binaries/mafft
@@ -3,7 +3,7 @@
 
 er=0;
 myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v6.717b (2009/12/03)"; export version
+version="v6.857b (2011/05/30)"; export version
 LANG=C; export LANG
 os=`uname`
 progname=`basename "$0"`
@@ -13,6 +13,8 @@ elif [ `echo $os | grep -i darwin` ]; then
 	os="darwin"
 elif [ `echo $os | grep -i sunos` ]; then
 	os="sunos"
+elif [ `echo $os | grep -i linux` ]; then
+	os="linux"
 else
 	os="unix"
 fi
@@ -21,7 +23,7 @@ export os
 if [ "$MAFFT_BINARIES" ]; then
 	prefix="$MAFFT_BINARIES"
 else
-	prefix=/usr/lib/mafft
+	prefix=/usr/libexec/mafft
 fi
 export prefix
 
@@ -129,6 +131,10 @@ elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
 	defaultiterate=2
 	defaultdistance="sixtuples"
 fi
+outputfile=""
+namelength=15
+anysymbol=0
+parallelizationstrategy="BAATARI2"
 kappa=$defaultkappa
 sbstmodel=$defaultsbstmodel
 fmodel=$defaultfmodel
@@ -193,13 +199,25 @@ 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=" "
@@ -211,6 +229,9 @@ if [ $# -gt 0 ]; then
 		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`
@@ -289,6 +310,37 @@ if [ $# -gt 0 ]; 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` 
@@ -436,7 +488,18 @@ if [ $# -gt 0 ]; then
 	fi
 	if [ $# -eq 1 ]; then
 		if [ -r "$1" -o "$1" = - ]; then
-			cat "$1" | tr "\r" "\n" > $TMPFILE/infile 
+
+			if [ -r "$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
@@ -449,13 +512,20 @@ if [ $# -gt 0 ]; then
 			while [ $# -gt 1 ];
 			do
 				shift
-				cat "$1" | tr "\r" "\n" >  $TMPFILE/seed$#
+				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
@@ -467,6 +537,15 @@ if [ $# -gt 0 ]; then
 	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`
@@ -489,8 +568,13 @@ if [ $# -gt 0 ]; then
 		fi
 	fi
 
-	if [ $iterate -gt 16 ]; then    #??
-		iterate=16
+	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
@@ -515,7 +599,7 @@ if [ $# -gt 0 ]; then
 #		echo "  Input format: fasta" 1>&2
 #		echo ""  1>&2
 #		echo "  Usage: `basename $0` [options] inputfile > outputfile" 1>&2
-	    echo "  http://align.bmr.kyushu-u.ac.jp/mafft/software/" 1>&2
+	    echo "  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
@@ -523,7 +607,7 @@ if [ $# -gt 0 ]; then
 #		echo ""  1>&2
 		echo "High speed:" 1>&2
 		echo "  % mafft in > out" 1>&2
-		echo "  % mafft --retree 1 in > out (fastest)" 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
@@ -540,6 +624,7 @@ if [ $# -gt 0 ]; then
 		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 
@@ -759,7 +844,7 @@ if [ $# -gt 0 ]; then
 		cycle=3
 	fi
 
-	if [ $nseq -gt 1000 -a $iterate -gt 1 ]; then
+	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
@@ -772,6 +857,19 @@ if [ $# -gt 0 ]; 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=" "
@@ -834,6 +932,10 @@ if [ $# -gt 0 ]; 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
@@ -843,6 +945,23 @@ if [ $# -gt 0 ]; then
 		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
@@ -931,20 +1050,35 @@ if [ $# -gt 0 ]; then
 	fi
 
 	if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
-		outputopt=" -c $strategy -r order  "
+		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 order "
+		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
@@ -956,7 +1090,13 @@ if [ $# -gt 0 ]; then
 				do
 					shift
 #					echo "num="$#
-					"$prefix/multi2hat3s" -t $nseq  -o $seedoffset -i seed$# >> infile 2>/dev/null || exit 1
+
+					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`
@@ -964,15 +1104,22 @@ if [ $# -gt 0 ]; then
 #					echo "seedoffset="$seedoffset
 				done;
 #				echo "seedoffset="$seedoffset
-				cat infile2 >> infile
+				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" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
+				"$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
@@ -980,65 +1127,65 @@ if [ $# -gt 0 ]; then
 				"$prefix/dndfast7" $swopt < infile > /dev/null  2>&1      || exit 1
 				cat hat3.seed hat3 > hatx
 				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "foldalignlocal" ]; then
-				"$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "foldalignglobal" ]; then
-				"$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "slara" ]; then
-				"$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "lara" ]; then
-				"$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "scarna" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null  2>&1      || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "global" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -F < infile > /dev/null  2>&1      || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "local" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $lexp -f $lgop  -h $laof -L < infile > /dev/null  2>&1      || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "globalgenaf" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null 2>&1    || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "localgenaf" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null  2>&1      || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "distonly" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null  2>&1      || exit 1
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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" $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $algopt $treealg < infile   > pre 2>/dev/null || exit 1
+				"$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 ]
@@ -1047,19 +1194,29 @@ if [ $# -gt 0 ]; then
 					mv pre infile
 					"$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre 2>/dev/null || exit 1
 				else
-					"$prefix/tbfast" $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model  -f "-"$gop  -h "-"$aof $param_fft  $localparam $algopt -J $treealg < pre > /dev/null 2>&1 || exit 1
+					"$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"       < pre     > /dev/null 2>&1 || exit 1
+				    "$prefix/dndpre" -C $numthreads < pre     > /dev/null 2>&1 || exit 1
 				fi
-				"$prefix/dvtditr" $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof  -I $iterate $weightopt $treeinopt $algoptit $treealg < pre     > /dev/null 2>&1 || exit 1
+				"$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
@@ -1071,7 +1228,13 @@ if [ $# -gt 0 ]; then
 				do
 					shift
 #					echo "num="$#
-					"$prefix/multi2hat3s" -t $nseq  -o $seedoffset -i seed$# >> infile  || exit 1
+
+					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`
@@ -1079,15 +1242,21 @@ if [ $# -gt 0 ]; then
 #					echo "seedoffset="$seedoffset
 				done;
 #				echo "seedoffset="$seedoffset
-				cat infile2 >> infile
+				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" -d "$prefix" -i infile > hat4  || exit 1
+				"$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
@@ -1095,65 +1264,65 @@ if [ $# -gt 0 ]; then
 				"$prefix/dndfast7" $swopt < infile > /dev/null     || exit 1
 				cat hat3.seed hat3 > hatx
 				mv hatx hat3
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
+				"$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 [ $distance = "foldalignlocal" ]; then
-				"$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "foldalignglobal" ]; then
-				"$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $pgexp -f $pggop  -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "slara" ]; then
-				"$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "lara" ]; then
-				"$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "scarna" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null   || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam   $algopt $treealg < infile   > /dev/null 2>&1 || exit 1
+				"$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 [ $distance = "global" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof   -F  < infile > /dev/null     || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
+				"$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 [ $distance = "local" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $lexp -f $lgop  -h $laof -L  < infile > /dev/null     || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
+				"$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 [ $distance = "globalgenaf" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null     || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
+				"$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 [ $distance = "localgenaf" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model  -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N  < infile > /dev/null     || exit 1
+				"$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" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
+				"$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 [ $distance = "distonly" ]; then
-				"$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null            || exit 1
-				"$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
+				"$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" $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft  $algopt $treealg < infile   > pre || exit 1
+				"$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
 
@@ -1163,30 +1332,95 @@ if [ $# -gt 0 ]; then
 					mv pre infile
 					"$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile  > pre || exit 1
 				else
-					"$prefix/tbfast" $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model  -f "-"$gop  -h "-"$aof $param_fft $localparam $algopt -J $treealg < pre > /dev/null || exit 1
+					"$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"       < pre     > /dev/null 2>&1 || exit 1
+			    	"$prefix/dndpre" -C $numthreads < pre     > /dev/null 2>&1 || exit 1
 				fi
-				"$prefix/dvtditr" $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -h "-"$aof -I $iterate $weightopt $treeinopt $algoptit $treealg < pre     > /dev/null || exit 1
+				"$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 < pre || exit 1
+			cat < $TMPFILE/pre || exit 1
 		else
-			"$prefix/f2cl" $outputopt < pre || exit 1
+			"$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"
@@ -1196,60 +1430,6 @@ if [ $# -gt 0 ]; then
 		cp $TMPFILE/hat2 "$infilename.hat2"
 	fi
 
-	if [ $quiet -eq 0 ]; then
-		echo '' 1>&2
-		if [ $mccaskill -eq 1 ]; then
-			echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>&2
-			echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>&2
-			echo "incorporated in the iterative alignment process (4)." 1>&2
-			echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>&2
-			echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>&2
-			echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>&2
-			echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
-			echo "" 1>&2
-		elif [ $contrafold -eq 1 ]; then
-			echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>&2
-			echo "and then incorporated in the iterative alignment process (4)." 1>&2
-			echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>&2
-			echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
-			echo "" 1>&2
-		fi
-		if [ $distance = "fasta" -o $partdist = "fasta" ]; then
-			echo "Pairwise alignments were computed by FASTA" 1>&2
-			echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>&2
-		fi
-		if [ $distance = "blast" ]; then
-			echo "Pairwise alignments were computed by BLAST" 1>&2
-			echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>&2
-		fi
-		if [ $distance = "scarna" ]; then
-			echo "Pairwise alignments were computed by MXSCARNA" 1>&2
-			echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>&2
-		fi
-		if [ $distance = "lara" -o $distance = "slara" ]; then
-			echo "Pairwise alignments were computed by LaRA" 1>&2
-			echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>&2
-		fi
-		if [ $distance = "foldalignlocal" ]; then
-			echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>&2
-			echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
-		fi
-		if [ $distance = "foldalignglobal" ]; then
-			echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>&2
-			echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
-		fi
-		printf "\n" 1>&2
-		echo 'Strategy:' 1>&2
-		printf ' '$strategy 1>&2
-		echo ' ('$performance')' 1>&2
-		echo ' '$explanation 1>&2
-		echo '' 1>&2
-		echo "If unsure which option to use, try 'mafft --auto input > output'." 1>&2
-#		echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>&2
-		echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>&2
-		echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>&2
-		echo '' 1>&2
-	fi
 	exit 0;
 fi
 
@@ -1265,25 +1445,15 @@ if [ -x "$tmpawk" ]; then
 	prog="$tmpawk"
 fi
 
-echo "prog="$prog 1>&2
+#echo "prog="$prog 1>&2
 
 umask 077
-export defaultaof
-export defaultgop
-export defaultfft
-export defaultcycle
-export defaultiterate
 (
 $prog '
 BEGIN {
 	prefix = ENVIRON["prefix"];
 	version = ENVIRON["version"];
 	myself = ENVIRON["myself"];
-	defaultgop = ENVIRON["defaultgop"]
-	defaultaof = ENVIRON["defaultaof"]
-	defaultfft = ENVIRON["defaultfft"]
-	defaultcycle = ENVIRON["defaultcycle"]
-	defaultiterate = ENVIRON["defaultiterate"]
 	while( 1 )
 	{
 		options = ""
@@ -1292,9 +1462,9 @@ BEGIN {
 		printf( "\n" )                                                                           > "/dev/tty";
 		printf( "   MAFFT %s\n", version )                                                       > "/dev/tty";
 		printf( "\n" )                                                                           > "/dev/tty";
-		printf( "        Copyright (c) 2009 Kazutaka Katoh\n" )                                  > "/dev/tty";
+		printf( "        Copyright (c) 2011 Kazutaka Katoh\n" )                                  > "/dev/tty";
 		printf( "        NAR 30:3059-3066, NAR 33:511-518\n" )                                   > "/dev/tty";
-		printf( "        http://align.bmr.kyushu-u.ac.jp/mafft/software/\n" )       > "/dev/tty";
+		printf( "        http://mafft.cbrc.jp/alignment/software/\n" )       > "/dev/tty";
 		printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
 		printf( "\n" ) > "/dev/tty";
 	
@@ -1306,13 +1476,15 @@ BEGIN {
 			close( "/dev/tty" )
 			if( res == 0 || NF == 0 )
 				continue;
-			infile0 = sprintf( "%s", $1 );
-			infile = sprintf( "%s", $1 );
+			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
@@ -1334,178 +1506,129 @@ BEGIN {
 				continue;
 			else
 			{
-				outfile = sprintf( "%s", $1 );
+				outfile = sprintf( "%s", $0 );
 				printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
 				break;
 			}
 		}
 	
-	
 		while( 1 )
 		{
-			retree = defaultcycle
+			outargs = "";
 			printf( "\n" ) > "/dev/tty";
-			printf( "Number of tree-rebuilding?\n" ) > "/dev/tty";
-			printf( "@ [%d] ", retree ) > "/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" );
-			if( res == 0 )
+#			printf( "res=%d, NF=%d\n", res, NF );
+
+			resnum = 0 + $1;
+#			printf( "resnum=%d\n", resnum );
+
+			if( resnum < 1 || 6 < resnum )
 				continue;
-			else if( NF == 0 )
-				;
-			else
-				retree = 0 + $1;
-			if( retree < 1 || 10 < retree )
-				;
 			else
 			{
-				printf( "OK. %d\n\n", retree ) > "/dev/tty";
+				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 )
 		{
-			niterate = defaultiterate;
+			arguments = "";
 			printf( "\n" ) > "/dev/tty";
-			printf( "Maximum number of iterations?\n" ) > "/dev/tty";
-			printf( "@ [%d] ", niterate ) > "/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" );
-			if( res == 0 )
+#			printf( "res=%d, NF=%d\n", res, NF );
+
+			resnum = 0 + $1;
+#			printf( "resnum=%d\n", resnum );
+
+			if( resnum < 1 || 6 < resnum )
 				continue;
-			else if( NF == 0 )
-				;
-			else
-				niterate = 0 + $1;
-			if( niterate < 0 || 1000 < niterate )
-				;
 			else
 			{
-				printf( "OK. %d\n\n", niterate ) > "/dev/tty";
+				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 )
-		{
-			fft = defaultfft;
-			printf( "\n" ) > "/dev/tty";
-			printf( "Use fft?\n" ) > "/dev/tty";
-			printf( "@ [%s] ", fft?"Yes":"No" ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 0 )
-			{
-				break;
-			}
-			else if( NF == 0 || $0 ~ /^[Yy]/ )
-			{
-				fft = 1;
-				break;
-			}
-			else if( NF == 0 || $0 ~ /^[Nn]/ )
-			{
-				fft = 0;
-				break;
-			}
-		}
-		if( fft )
-		{
-				printf( "OK. FFT is enabled.\n\n" ) > "/dev/tty";
-				fftparam = " ";
-		}
-		else
-		{
-				printf( "OK. FFT is disabled.\n\n" ) > "/dev/tty";
-				fftparam = " --nofft ";
-		}
 
 		while( 1 )
 		{
-			scoringmatrix = 3;
 			printf( "\n" ) > "/dev/tty";
-			printf( "Scoring matrix? (ignored when DNA sequence is input.)\n" ) > "/dev/tty";
-			printf( " 1. BLOSUM 30\n" ) > "/dev/tty";
-			printf( " 2. BLOSUM 45\n" ) > "/dev/tty";
-			printf( " 3. BLOSUM 62\n" ) > "/dev/tty";
-			printf( " 4. BLOSUM 80\n" ) > "/dev/tty";
-			printf( " 5. JTT 200\n" ) > "/dev/tty";
-			printf( " 6. JTT 100\n" ) > "/dev/tty";
-			printf( "@ [%d] ", scoringmatrix ) > "/dev/tty";
+			printf( "Additional arguments? (--ep #, --op #, --kappa #, etc)\n" ) > "/dev/tty";
+			printf( "@ " ) > "/dev/tty";
 			res = getline < "/dev/tty";
 			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 0 )
-				;
-			else
-				scoringmatrix = 0 + $1;
-			if( scoringmatrix < 1 || 6 < scoringmatrix )
-				;
-			else
+			if( res == 0 || NF == 0 )
 			{
 				break;
 			}
-		}
-		if( scoringmatrix == 1 )
-			scoringparam = " --bl 30 ";
-		else if( scoringmatrix == 2 )
-			scoringparam = " --bl 45 ";
-		else if( scoringmatrix == 3 )
-			scoringparam = " --bl 62 ";
-		else if( scoringmatrix == 4 )
-			scoringparam = " --bl 80 ";
-		else if( scoringmatrix == 5 )
-			scoringparam = " --jtt 200 ";
-		else if( scoringmatrix == 6 )
-			scoringparam = " --jtt 100 ";
-		printf( "OK. %s\n\n",scoringparam ) > "/dev/tty";
-	
-		while( 1 )
-		{
-			penalty = 0.0 + defaultgop;
-			offset = 0.0 + defaultaof;
-			printf( "\n" ) > "/dev/tty";
-			printf( "Parameters (gap opening penalty, offset)?\n", penalty, offset ) > "/dev/tty";
-			printf( "@ [%5.3f, %5.3f] ", penalty, offset ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 2 )
-			{
-				penalty = 0.0 + $1;
-				offset = 0.0 + $2;
-			}
-			else if( NF == 0 )
-				;
-			else
-				continue;
-			if( penalty < 0.0 || 10.0 < penalty )
-				;
-			else if( offset < 0.0 || 10.0 < offset )
-				;
 			else
 			{
-				printf( "OK. %5.3f %5.3f\n\n", penalty, offset ) > "/dev/tty";
+				addargs = sprintf( "%s", $0 );
+				printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty";
 				break;
 			}
 		}
-	
-		command = sprintf( "\"%s\" %s --retree %d --maxiterate %d %s --op %f --ep %f %s > %s", myself, fftparam, retree, niterate, scoringparam, penalty, offset, infile, outfile );
+
+		arguments = sprintf( "%s %s %s", addargs, arguments, outargs );
+
+		print ""
+		command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile );
 		gsub( /\\/, "/", command );
 
 
-		printf( "%s\n\n", command ) > "/dev/tty";
+		printf( "command=\n%s\n", command ) > "/dev/tty";
 	
 	
 		while( 1 )
 		{
 			go = 0;
-			printf( "\n" ) > "/dev/tty";
 			printf( "OK?\n" ) > "/dev/tty";
 			printf( "@ [Y] " ) > "/dev/tty";
 			res = getline < "/dev/tty";
@@ -1525,6 +1648,8 @@ BEGIN {
 		printf( "\n" ) > "/dev/tty";
 	}
 	system( command );
+	command = sprintf( "less \"%s\"", outfile );
+	system( command );
 	printf( "Press Enter to exit." ) > "/dev/tty";
 	res = getline < "/dev/tty";
 }