binaries/linuxIA32/mafft/mafft

   1 #! /bin/sh
   2
   3
   4 er=0;
   5 myself=`dirname "$0"`/`basename "$0"`; export myself
   6 version="v6.717b (2009/12/03)"; export version
   7 LANG=C; export LANG
   8 os=`uname`
   9 progname=`basename "$0"`
  10 if [ `echo $os | grep -i cygwin` ]; then
  11         os="cygwin"
  12 elif [ `echo $os | grep -i darwin` ]; then
  13         os="darwin"
  14 elif [ `echo $os | grep -i sunos` ]; then
  15         os="sunos"
  16 else
  17         os="unix"
  18 fi
  19 export os
  20
  21 if [ "$MAFFT_BINARIES" ]; then
  22         prefix="$MAFFT_BINARIES"
  23 else
  24         prefix=/usr/lib/mafft
  25 fi
  26 export prefix
  27
  28 if [ $# -gt 0 ]; then
  29         if [ "$1" = "--man" ]; then
  30                 man "$prefix/mafft.1"
  31                 exit 0;
  32         fi
  33 fi
  34
  35 if [ ! -x "$prefix/tbfast" ]; then
  36         echo "" 1>&2
  37         echo "correctly installed?" 1>&2
  38         echo "mafft binaries have to be installed in \$MAFFT_BINARIES" 1>&2
  39         echo "or the $prefix directory". 1>&2
  40         echo "" 1>&2
  41         exit 1
  42         er=1
  43 fi
  44
  45 defaultiterate=0
  46 defaultcycle=2
  47 defaultgop="1.53"
  48 #defaultaof="0.123"
  49 defaultaof="0.000"
  50 defaultlaof="0.100"
  51 defaultlgop="-2.00"
  52 defaultfft=1
  53 defaultrough=0
  54 defaultdistance="sixtuples"
  55 #defaultdistance="local"
  56 defaultweighti="2.7"
  57 defaultweightr="0.0"
  58 defaultweightm="1.0"
  59 defaultmccaskill=0
  60 defaultcontrafold=0
  61 defaultalgopt="  "
  62 defaultalgoptit="  "
  63 defaultsbstmodel=" -b 62 "
  64 defaultfmodel=" "
  65 defaultkappa=" "
  66 if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then
  67         defaultfft=1
  68         defaultcycle=1
  69         defaultiterate=1000
  70         defaultdistance="scarna"
  71         defaultweighti="3.2"
  72         defaultweightr="8.0"
  73         defaultweightm="2.0"
  74         defaultmccaskill=1
  75         defaultcontrafold=0
  76         defaultalgopt=" -A "
  77         defaultalgoptit=" -AB " ## chui
  78         defaultaof="0.0"
  79         defaultsbstmodel=" -b 62 "
  80         defaultkappa=" "
  81         defaultfmodel=" -a "
  82 elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
  83         defaultfft=1
  84         defaultcycle=1
  85         defaultiterate=1000
  86         defaultdistance="global"
  87         defaultweighti="3.2"
  88         defaultweightr="8.0"
  89         defaultweightm="2.0"
  90         defaultmccaskill=1
  91         defaultcontrafold=0
  92         defaultalgopt=" -A "
  93         defaultalgoptit=" -AB " ## chui
  94         defaultaof="0.0"
  95         defaultsbstmodel=" -b 62 "
  96         defaultkappa=" "
  97         defaultfmodel=" -a "
  98 elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
  99         defaultfft=0
 100         defaultcycle=1
 101         defaultiterate=1000
 102         defaultdistance="local"
 103 elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then
 104         defaultfft=1
 105         defaultcycle=1
 106         defaultiterate=1000
 107         defaultdistance="global"
 108 elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then
 109         defaultfft=0
 110         defaultcycle=1
 111         defaultiterate=1000
 112         defaultdistance="localgenaf"
 113 elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
 114         defaultfft=1
 115         defaultcycle=2
 116         defaultdistance="sixtuples"
 117 elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
 118         defaultfft=1
 119         defaultcycle=2
 120         defaultiterate=2
 121         defaultdistance="sixtuples"
 122 elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
 123         defaultfft=0
 124         defaultcycle=2
 125         defaultdistance="sixtuples"
 126 elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
 127         defaultfft=0
 128         defaultcycle=2
 129         defaultiterate=2
 130         defaultdistance="sixtuples"
 131 fi
 132 kappa=$defaultkappa
 133 sbstmodel=$defaultsbstmodel
 134 fmodel=$defaultfmodel
 135 gop=$defaultgop
 136 aof=$defaultaof
 137 cycle=$defaultcycle
 138 iterate=$defaultiterate
 139 fft=$defaultfft
 140 rough=$defaultrough
 141 distance=$defaultdistance
 142 forcefft=0
 143 memopt=" "
 144 weightopt=" "
 145 GGOP="-6.00"
 146 LGOP="-6.00"
 147 LEXP="-0.000"
 148 GEXP="-0.000"
 149 lgop=$defaultlgop
 150 lexp="-0.100"
 151 laof=$defaultlaof
 152 pggop="-2.00"
 153 pgexp="-0.10"
 154 pgaof="0.10"
 155 rgop="-1.530"
 156 rgep="-0.000"
 157 seqtype="  "
 158 weighti=$defaultweighti
 159 weightr=$defaultweightr
 160 weightm=$defaultweightm
 161 rnaalifold=0
 162 mccaskill=$defaultmccaskill
 163 contrafold=$defaultcontrafold
 164 quiet=0
 165 debug=0
 166 sw=0
 167 algopt=$defaultalgopt
 168 algoptit=$defaultalgoptit
 169 scorecalcopt=" "
 170 coreout=0
 171 corethr="0.5"
 172 corewin="100"
 173 coreext=" "
 174 outputformat="pir"
 175 outorder="input"
 176 seed="x"
 177 seedtable="x"
 178 auto=0
 179 groupsize=-1
 180 partsize=50
 181 partdist="sixtuples"
 182 partorderopt=" -x "
 183 treeout=0
 184 distout=0
 185 treein=0
 186 topin=0
 187 treeinopt="  "
 188 seedfiles="/dev/null"
 189 seedtablefile="/dev/null"
 190 aamatrix="/dev/null"
 191 treeinfile="/dev/null"
 192 rnascoremtx=" "
 193 laraparams="/dev/null"
 194 foldalignopt=" "
 195 treealg=" -X "
 196 if [ $# -gt 0 ]; then
 197         while [ $# -gt 1 ];
 198         do
 199                 if [ "$1" = "--auto" ]; then
 200                         auto=1
 201                 elif [ "$1" = "--clustalout" ]; then
 202                         outputformat="clustal"
 203                 elif [ "$1" = "--reorder" ]; then
 204                         outorder="aligned"
 205                         partorderopt=" "
 206                 elif [ "$1" = "--inputorder" ]; then
 207                         outorder="input"
 208                         partorderopt=" -x "
 209                 elif [ "$1" = "--unweight" ]; then
 210                         weightopt=" -u "
 211                 elif [ "$1" = "--algq" ]; then
 212                         algopt=" -Q "
 213                         algoptit=" -QB "
 214                 elif [ "$1" = "--groupsize" ]; then
 215                         shift
 216                         groupsize=`expr "$1" - 0`
 217                 elif [ "$1" = "--partsize" ]; then
 218                         shift
 219                         partsize=`expr "$1" - 0`
 220                 elif [ "$1" = "--parttree" ]; then
 221                         distance="parttree"
 222                         partdist="sixtuples"
 223                 elif [ "$1" = "--dpparttree" ]; then
 224                         distance="parttree"
 225                         partdist="localalign"
 226                 elif [ "$1" = "--fastaparttree" ]; then
 227                         distance="parttree"
 228                         partdist="fasta"
 229                 elif [ "$1" = "--treeout" ]; then
 230                         treeout=1
 231                 elif [ "$1" = "--distout" ]; then
 232                         distout=1
 233                 elif [ "$1" = "--fastswpair" ]; then
 234                         distance="fasta"
 235                         sw=1
 236                 elif [ "$1" = "--fastapair" ]; then
 237                         distance="fasta"
 238                         sw=0
 239                 elif [ "$1" = "--averagelinkage" ]; then
 240                         treealg=" -E "
 241                 elif [ "$1" = "--minimumlinkage" ]; then
 242                         treealg=" -q "
 243                 elif [ "$1" = "--noscore" ]; then
 244                         scorecalcopt=" -Z "
 245                 elif [ "$1" = "--6merpair" ]; then
 246                         distance="sixtuples"
 247                 elif [ "$1" = "--blastpair" ]; then
 248                         distance="blast"
 249                 elif [ "$1" = "--globalpair" ]; then
 250                         distance="global"
 251                 elif [ "$1" = "--localpair" ]; then
 252                         distance="local"
 253                 elif [ "$1" = "--scarnapair" ]; then
 254                         distance="scarna"
 255                 elif [ "$1" = "--larapair" ]; then
 256                         distance="lara"
 257                 elif [ "$1" = "--slarapair" ]; then
 258                         distance="slara"
 259                 elif [ "$1" = "--foldalignpair" ]; then
 260                         distance="foldalignlocal"
 261                 elif [ "$1" = "--foldalignlocalpair" ]; then
 262                         distance="foldalignlocal"
 263                 elif [ "$1" = "--foldalignglobalpair" ]; then
 264                         distance="foldalignglobal"
 265                 elif [ "$1" = "--globalgenafpair" ]; then
 266                         distance="globalgenaf"
 267                 elif [ "$1" = "--localgenafpair" ]; then
 268                         distance="localgenaf"
 269                 elif [ "$1" = "--genafpair" ]; then
 270                         distance="localgenaf"
 271                 elif [ "$1" = "--memsave" ]; then
 272                         memopt=" -M -B "         # -B (bunkatsunashi no riyu ga omoidasenai)
 273                 elif [ "$1" = "--nomemsave" ]; then
 274                         memopt=" -N "
 275                 elif [ "$1" = "--nuc" ]; then
 276                         seqtype=" -D "
 277                 elif [ "$1" = "--amino" ]; then
 278                         seqtype=" -P "
 279                 elif [ "$1" = "--fft" ]; then
 280                         fft=1
 281                         forcefft=1
 282                 elif [ "$1" = "--nofft" ]; then
 283                         fft=0
 284                 elif [ "$1" = "--quiet" ]; then
 285                         quiet=1
 286                 elif [ "$1" = "--debug" ]; then
 287                         debug=1
 288                 elif [ "$1" = "--coreext" ]; then
 289                         coreext=" -c "
 290                 elif [ "$1" = "--core" ]; then
 291                         coreout=1
 292                 elif [ "$1" = "--maxiterate" ]; then
 293                         shift
 294                         iterate=`expr "$1" - 0`
 295                 elif [ "$1" = "--retree" ]; then
 296                         shift
 297                         cycle=`expr "$1" - 0`
 298                 elif [ "$1" = "--aamatrix" ]; then
 299                         shift
 300                         sbstmodel=" -b -1 "
 301                         aamatrix="$1"
 302                 elif [ "$1" = "--treein" ]; then
 303                         shift
 304                         treeinopt=" -U "
 305                         treein=1
 306                         treeinfile="$1"
 307                 elif [ "$1" = "--topin" ]; then
 308                         shift
 309                         treeinopt=" -V "
 310                         treein=1
 311                         treeinfile="$1"
 312                         echo "The --topin option has been disabled." 1>&2
 313                         echo "There was a bug in version < 6.530."   1>&2
 314                         echo "This bug has not yet been fixed."      1>&2
 315                         exit 1
 316                 elif [ "$1" = "--kappa" ]; then
 317                         shift
 318                         kappa=" -k $1 "
 319                 elif [ "$1" = "--fmodel" ]; then
 320                         fmodel=" -a "
 321                 elif [ "$1" = "--jtt" ]; then
 322                         shift
 323                         sbstmodel=" -j $1"
 324                 elif [ "$1" = "--kimura" ]; then
 325                         shift
 326                         sbstmodel=" -j $1"
 327                 elif [ "$1" = "--tm" ]; then
 328                         shift
 329                         sbstmodel=" -m $1"
 330                 elif [ "$1" = "--bl" ]; then
 331                         shift
 332                         sbstmodel=" -b $1"
 333                 elif [ "$1" = "--weighti" ]; then
 334                         shift
 335                         weighti="$1"
 336                 elif [ "$1" = "--weightr" ]; then
 337                         shift
 338                         weightr="$1"
 339                 elif [ "$1" = "--weightm" ]; then
 340                         shift
 341                         weightm="$1"
 342                 elif [ "$1" = "--rnaalifold" ]; then
 343                         rnaalifold=1
 344                 elif [ "$1" = "--mccaskill" ]; then
 345                         mccaskill=1
 346                         contrafold=0
 347                 elif [ "$1" = "--contrafold" ]; then
 348                         mccaskill=0
 349                         contrafold=1
 350                 elif [ "$1" = "--ribosum" ]; then
 351                         rnascoremtx=" -s "
 352                 elif [ "$1" = "--op" ]; then
 353                         shift
 354                         gop="$1"
 355                 elif [ "$1" = "--ep" ]; then
 356                         shift
 357                         aof="$1"
 358                 elif [ "$1" = "--rop" ]; then
 359                         shift
 360                         rgop="$1"
 361                 elif [ "$1" = "--rep" ]; then
 362                         shift
 363                         rgep="$1"
 364                 elif [ "$1" = "--lop" ]; then
 365                         shift
 366                         lgop="$1"
 367                 elif [ "$1" = "--LOP" ]; then
 368                         shift
 369                         LGOP="$1"
 370                 elif [ "$1" = "--lep" ]; then
 371                         shift
 372                         laof="$1"
 373                 elif [ "$1" = "--lexp" ]; then
 374                         shift
 375                         lexp="$1"
 376                 elif [ "$1" = "--LEXP" ]; then
 377                         shift
 378                         LEXP="$1"
 379                 elif [ "$1" = "--GEXP" ]; then
 380                         shift
 381                         GEXP="$1"
 382                 elif [ "$1" = "--GOP" ]; then
 383                         shift
 384                         GGOP="$1"
 385                 elif [ "$1" = "--gop" ]; then
 386                         shift
 387                         pggop="$1"
 388                 elif [ "$1" = "--gep" ]; then
 389                         shift
 390                         pgaof="$1"
 391                 elif [ "$1" = "--gexp" ]; then
 392                         shift
 393                         pgexp="$1"
 394                 elif [ "$1" = "--laraparams" ]; then
 395                         shift
 396                         laraparams="$1"
 397                 elif [ "$1" = "--corethr" ]; then
 398                         shift
 399                         corethr="$1"
 400                 elif [ "$1" = "--corewin" ]; then
 401                         shift
 402                         corewin="$1"
 403                 elif [ "$1" = "--seedtable" ]; then
 404                         shift
 405                         seedtable="y"
 406                         seedtablefile="$1"
 407                 elif [ "$1" = "--seed" ]; then
 408                         shift
 409                         seed="m"
 410                         seedfiles="$seedfiles $1"
 411                 elif [ $progname = "fftns" -o  $progname = "nwns" ]; then
 412                         if [ "$1" -gt 0 ]; then
 413                                 cycle=`expr "$1" - 0`
 414                         fi
 415                 else
 416                         echo "Unknown option:  $1" 1>&2
 417                         er=1;
 418                 fi
 419                 shift
 420         done;
 421
 422
 423
 424 #       TMPFILE=/tmp/$progname.$$
 425         TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`
 426         if [ $? -ne 0 ]; then
 427                 echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
 428                 TMPFILE=`mktemp -d /tmp/$progname.XXXXXXXXXX`
 429         fi
 430         umask 077
 431 #       mkdir  $TMPFILE  || er=1
 432         if [ $debug -eq 1 ]; then
 433                 trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0
 434         else
 435                 trap "rm -rf $TMPFILE " 0
 436         fi
 437         if [ $# -eq 1 ]; then
 438                 if [ -r "$1" -o "$1" = - ]; then
 439                         cat "$1" | tr "\r" "\n" > $TMPFILE/infile
 440                         cat "$aamatrix"       | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_aamtx
 441                         cat "$treeinfile"     | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_guidetree
 442                         cat "$seedtablefile"  | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_seedtablefile
 443                         cat "$laraparams"     | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_lara.params
 444 #                       echo $seedfiles
 445                         infilename="$1"
 446                         seedfilesintmp="/dev/null"
 447                         seednseq="0"
 448                         set $seedfiles > /dev/null
 449                         while [ $# -gt 1 ];
 450                         do
 451                                 shift
 452                                 cat "$1" | tr "\r" "\n" >  $TMPFILE/seed$#
 453                                 seednseq=$seednseq" "`grep -c '^[>|=]' $TMPFILE/seed$#`
 454                                 seedfilesintmp=$seedfilesintmp" "seed$#
 455                         done
 456 #                       ls $TMPFILE
 457 #                       echo $seedfilesintmp
 458 #                       echo $seednseq
 459                 else
 460                         echo "$0": Cannot open "$1". 1>&2
 461                         er=1
 462 #                       exit 1;
 463                 fi
 464         else
 465                 echo '$#'"=$#" 1>&2
 466                 er=1
 467         fi
 468
 469
 470         if [ $auto -eq 1 ]; then
 471                 "$prefix/countlen" < $TMPFILE/infile > $TMPFILE/size
 472                 nseq=`awk '{print $1}' $TMPFILE/size`
 473                 nlen=`awk '{print $3}' $TMPFILE/size`
 474                 if [ $nlen -lt 2000 -a $nseq -lt 100 ]; then
 475                         distance="local"
 476                         iterate=1000
 477                 elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
 478                         distance="sixtuples"
 479                         iterate=2
 480                 else
 481                         distance="sixtuples"
 482                         iterate=0
 483                 fi
 484                 if [ $quiet -eq 0 ]; then
 485                         echo "nseq = " $nseq              1>&2
 486                         echo "nlen = " $nlen              1>&2
 487                         echo "distance = " $distance      1>&2
 488                         echo "iterate = " $iterate        1>&2
 489                 fi
 490         fi
 491
 492         if [ $iterate -gt 16 ]; then    #??
 493                 iterate=16
 494         fi
 495
 496         if [ $rnaalifold -eq 1 ]; then
 497                 rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx "
 498 #               rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R "
 499                 rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R "
 500         elif [ $mccaskill -eq 1 -o $contrafold -eq 1 ]; then
 501                 rnaopt=" -o $rgop -c $weightm -r $weightr "
 502 #               rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx "
 503                 rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx "
 504         else
 505                 rnaopt="  "
 506                 rnaoptit=" -F "
 507         fi
 508
 509         model="$sbstmodel $kappa $fmodel"
 510
 511         if [ $er -eq 1 ]; then
 512                 echo "------------------------------------------------------------------------------" 1>&2
 513                 echo "  MAFFT" $version 1>&2
 514 #               echo "" 1>&2
 515 #               echo "  Input format: fasta" 1>&2
 516 #               echo ""  1>&2
 517 #               echo "  Usage: `basename $0` [options] inputfile > outputfile" 1>&2
 518             echo "  http://align.bmr.kyushu-u.ac.jp/mafft/software/" 1>&2
 519                 echo "  NAR 30:3059-3066 (2002), Briefings in Bioinformatics 9:286-298 (2008)"        1>&2
 520 #               echo "------------------------------------------------------------------------------" 1>&2
 521 #               echo "  % mafft in > out" 1>&2
 522                 echo "------------------------------------------------------------------------------" 1>&2
 523 #               echo ""  1>&2
 524                 echo "High speed:" 1>&2
 525                 echo "  % mafft in > out" 1>&2
 526                 echo "  % mafft --retree 1 in > out (fastest)" 1>&2
 527                 echo "" 1>&2
 528                 echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2
 529                 echo "  % mafft --maxiterate 1000 --localpair  in > out (% linsi in > out is also ok)" 1>&2
 530                 echo "  % mafft --maxiterate 1000 --genafpair  in > out (% einsi in > out)" 1>&2
 531                 echo "  % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2
 532                 echo "" 1>&2
 533                 echo "If unsure which option to use:" 1>&2
 534                 echo "  % mafft --auto in > out" 1>&2
 535                 echo "" 1>&2
 536 #               echo "Other options:" 1>&2
 537                 echo "--op # :         Gap opening penalty, default: 1.53" 1>&2
 538                 echo "--ep # :         Offset (works like gap extension penalty), default: 0.0" 1>&2
 539                 echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 1>&2
 540                 echo "--clustalout :   Output: clustal format, default: fasta" 1>&2
 541                 echo "--reorder :      Outorder: aligned, default: input order" 1>&2
 542                 echo "--quiet :        Do not report progress" 1>&2
 543 #               echo "" 1>&2
 544 #               echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2
 545 #               echo " most accurate in many cases, assumes only one alignable domain" 1>&2
 546 #               echo "" 1>&2
 547 #               echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2
 548 #               echo " works well if many unalignable residues exist between alignable domains" 1>&2
 549 #               echo "" 1>&2
 550 #               echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2
 551 #               echo " suitable for globally alignable sequences            " 1>&2
 552 #               echo "" 1>&2
 553 #               echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2
 554 #               echo " accurate and slow, iterative refinement method      " 1>&2
 555 #               echo "" 1>&2
 556 #               echo "If the input sequences are long (~1,000,000nt)," 1>&2
 557 #               echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2
 558 #               echo "" 1>&2
 559 #               echo "If many (~5,000) sequences are to be aligned," 1>&2
 560 #               echo "" 1>&2
 561 #               echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2
 562 #               echo "" 1>&2
 563 #               echo " --localpair :      All pairwise local alignment information is included"  1>&2
 564 #               echo "                    to the objective function, default: off"  1>&2
 565 #               echo " --globalpair :     All pairwise global alignment information is included"  1>&2
 566 #               echo "                    to the objective function, default: off"  1>&2
 567 #               echo " --op # :           Gap opening penalty, default: $defaultgop " 1>&2
 568 #               echo " --ep # :           Offset (works like gap extension penalty), default: $defaultaof " 1>&2
 569 #               echo " --bl #, --jtt # :  Scoring matrix, default: BLOSUM62" 1>&2
 570 #               echo "                    Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2
 571 #               echo "                    or JTT (--jtt) # PAM. " 1>&2
 572 #               echo " --nuc or --amino : Sequence type, default: auto" 1>&2
 573 #               echo " --retree # :       The number of tree building in progressive method " 1>&2
 574 #               echo "                    (see the paper for detail), default: $defaultcycle " 1>&2
 575 #               echo " --maxiterate # :   Maximum number of iterative refinement, default: $defaultiterate " 1>&2
 576 #               if [ $defaultfft -eq 1 ]; then
 577 #                       echo " --fft or --nofft:  FFT is enabled or disabled, default: enabled" 1>&2
 578 #               else
 579 #                       echo " --fft or --nofft:  FFT is enabled or disabled, default: disabled" 1>&2
 580 #               fi
 581 #               echo " --memsave:         Memory saving mode" 1>&2
 582 #               echo "                    (for long genomic sequences), default: off" 1>&2
 583 #               echo " --clustalout :     Output: clustal format, default: fasta" 1>&2
 584 #               echo " --reorder :        Outorder: aligned, default: input order" 1>&2
 585 #               echo " --quiet :          Do not report progress" 1>&2
 586 #               echo "-----------------------------------------------------------------------------" 1>&2
 587                 exit 1;
 588         fi
 589         if [ $sw -eq 1 ]; then
 590                 swopt=" -A "
 591         else
 592                 swopt=" "
 593         fi
 594
 595         if [ $distance = "fasta" -o $partdist = "fasta" ]; then
 596                 if [ ! "$FASTA_4_MAFFT" ]; then
 597                         FASTA_4_MAFFT=`which fasta34`
 598                 fi
 599
 600                 if [ ! -x "$FASTA_4_MAFFT" ]; then
 601                         echo ""       1>&2
 602                         echo "== Install FASTA ========================================================" 1>&2
 603                         echo "This option requires the fasta34 program (FASTA version x.xx or higher)"   1>&2
 604                         echo "installed in your PATH.  If you have the fasta34 program but have renamed" 1>&2
 605                         echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2
 606                         echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2
 607                         echo "=========================================================================" 1>&2
 608                         echo "" 1>&2
 609                         exit 1
 610                 fi
 611         fi
 612         if [ $distance = "lara" -o $distance = "slara" ]; then
 613                 if [ ! -x "$prefix/mafft_lara" ]; then
 614                         echo ""       1>&2
 615                         echo "== Install LaRA =========================================================" 1>&2
 616                         echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)."     1>&2
 617                         echo "The executable have to be renamed to 'mafft_lara' and installed into "     1>&2
 618                         echo "the $prefix directory. "                                                   1>&2
 619                         echo "A configuration file of LaRA also have to be given"                        1>&2
 620                         echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
 621                         echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
 622                         echo "=========================================================================" 1>&2
 623                         echo "" 1>&2
 624                         exit 1
 625                 fi
 626                 if [ ! -s "$laraparams" ]; then
 627                         echo ""       1>&2
 628                         echo "== Configure LaRA =======================================================" 1>&2
 629                         echo "A configuration file of LaRA have to be given"                             1>&2
 630                         echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
 631                         echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
 632                         echo "=========================================================================" 1>&2
 633                         echo "" 1>&2
 634                         exit 1
 635                 fi
 636         fi
 637         if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
 638         if [ ! -x "$prefix/foldalign210" ]; then
 639                         echo ""       1>&2
 640                         echo "== Install FOLDALIGN ====================================================" 1>&2
 641                         echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2
 642                         echo "The executable have to be renamed to 'foldalign210' and installed into "   1>&2
 643                         echo "the $prefix directory. "                                                   1>&2
 644                         echo "=========================================================================" 1>&2
 645                         echo "" 1>&2
 646                         exit 1
 647                 fi
 648         fi
 649         if [ $distance = "scarna" ]; then
 650                 if [ ! -x "$prefix/mxscarnamod" ]; then
 651                         echo ""       1>&2
 652                         echo "== Install MXSCARNA ======================================================" 1>&2
 653                         echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required."          1>&2
 654                         echo "Please 'make' at the 'extensions' directory of the MAFFT source package,"   1>&2
 655                         echo "which contains the modified version of MXSCARNA."                           1>&2
 656                         echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html "                1>&2
 657                         echo "==========================================================================" 1>&2
 658                         echo "" 1>&2
 659                         exit 1
 660                 fi
 661         fi
 662         if [ $mccaskill -eq 1 ]; then
 663                 if [ ! -x "$prefix/mxscarnamod" ]; then
 664                         echo ""       1>&2
 665                         echo "== Install MXSCARNA ======================================================" 1>&2
 666                         echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required."          1>&2
 667                         echo "Please 'make' at the 'extensions' directory of the MAFFT source package,"   1>&2
 668                         echo "which contains the modified version of MXSCARNA."                           1>&2
 669                         echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html "                1>&2
 670                         echo "==========================================================================" 1>&2
 671                         echo "" 1>&2
 672                         exit 1
 673                 fi
 674         fi
 675         if [ $contrafold -eq 1 ]; then
 676                 if [ ! -x "$prefix/contrafold" ]; then
 677                         echo ""       1>&2
 678                         echo "== Install CONTRAfold ===================================================" 1>&2
 679                         echo "This option requires CONTRAfold"                                           1>&2
 680                         echo "(Do et al. http://contra.stanford.edu/contrafold/)."                       1>&2
 681                         echo "The executable 'contrafold' have to be installed into "                    1>&2
 682                         echo "the $prefix directory. "                                                   1>&2
 683                         echo "=========================================================================" 1>&2
 684                         echo "" 1>&2
 685                         exit 1
 686                 fi
 687         fi
 688
 689 #old
 690 #       if [ $treeout -eq 1 ]; then
 691 #               parttreeoutopt="-t"
 692 #               if [ $cycle -eq 0 ]; then
 693 #                       treeoutopt="-t -T"
 694 #                       groupsize=1
 695 #                       iterate=0
 696 #                       if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
 697 #                               distance="distonly"
 698 #                       fi
 699 #               else
 700 #                       treeoutopt="-t"
 701 #               fi
 702 #       else
 703 #               parttreeoutopt=" "
 704 #               if [ $cycle -eq 0 ]; then
 705 #                       treeoutopt="-t -T"
 706 #                       iterate=0
 707 #                       if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
 708 #                               distance="distonly"
 709 #                       fi
 710 #               else
 711 #                       treeoutopt=" "
 712 #               fi
 713 #       fi
 714
 715 #new
 716         if [ $cycle -eq 0 ]; then
 717                 treeoutopt="-t -T"
 718                 iterate=0
 719                 if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
 720                         distance="distonly"
 721                 fi
 722                 if [ $treeout -eq 1 ]; then
 723                         parttreeoutopt="-t"
 724                         groupsize=1
 725                 else
 726                         parttreeoutopt=" "
 727                 fi
 728                 if [ $distout -eq 1 ]; then
 729                         distoutopt="-y -T"
 730                 fi
 731         else
 732                 if [ $treeout -eq 1 ]; then
 733                         parttreeoutopt="-t"
 734                         treeoutopt="-t"
 735                 else
 736                         parttreeoutopt=" "
 737                         treeoutopt=" "
 738                 fi
 739                 if [ $distout -eq 1 ]; then
 740                         distoutopt="-y"
 741                 fi
 742         fi
 743 #
 744
 745         formatcheck=`grep -c '^[[:blank:]]\+>' $TMPFILE/infile | head -1 `
 746         if [ $formatcheck -gt 0 ]; then
 747                 echo "The first character of a description line must be " 1>&2
 748                 echo "the greater-than (>) symbol, not a blank."           1>&2
 749                 echo "Please check the format around the following line(s):"  1>&2
 750                 grep -n '^[[:blank:]]\+>' $TMPFILE/infile  1>&2
 751                 exit 1
 752         fi
 753
 754         nseq=`grep -c '^[>|=]' $TMPFILE/infile | head -1 `
 755         if [ $nseq -eq 2 ]; then
 756                 cycle=1
 757         fi
 758         if [ $cycle -gt 3 ]; then
 759                 cycle=3
 760         fi
 761
 762         if [ $nseq -gt 1000 -a $iterate -gt 1 ]; then
 763                 echo "Too many sequences to perform iterative refinement!" 1>&2
 764                 echo "Please use a progressive method." 1>&2
 765                 exit 1
 766         fi
 767
 768
 769         if [ $distance = "sixtuples" -a \( $seed = "x" -a $seedtable = "x" \) ]; then
 770                 localparam=" "
 771         elif [ $distance = "sixtuples" -a \( $seed != "x" -o $seedtable != "x" \) ]; then
 772                 if [ $cycle -lt 2 ]; then
 773                         cycle=2                # nazeda
 774                 fi
 775                 localparam="-l "$weighti
 776         elif [ $distance = "parttree" ]; then
 777                 localparam=" "
 778                 if [ $groupsize -gt -1 ]; then
 779                         cycle=1
 780                 fi
 781         else
 782                 localparam=" -l "$weighti
 783                 if [ $cycle -gt 1 ]; then  # 09/01/08
 784                         cycle=1
 785                 fi
 786         fi
 787
 788         if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
 789                 aof="0.000"
 790         fi
 791
 792         if [ "$memopt" = " -M -B " -a "$distance" != "sixtuples" ]; then
 793                 echo "Impossible" 1>&2
 794                 exit 1
 795         fi
 796 #exit
 797
 798         if [ $distance = "parttree" ]; then
 799                 if [ $seed != "x" -o $seedtable != "x" ]; then
 800                         echo "Impossible" 1>&2
 801                         exit 1
 802                 fi
 803                 if [ $iterate -gt 1 ]; then
 804                         echo "Impossible" 1>&2
 805                         exit 1
 806                 fi
 807                 if [ $outorder = "aligned" ]; then
 808                         outorder="input"
 809                 fi
 810                 outorder="input"   # partorder ga kiku
 811                 if [ $partdist = "localalign" ]; then
 812                         splitopt=" -L "    # -L -l -> fast
 813                 elif [ $partdist = "fasta" ]; then
 814                         splitopt=" -S "
 815                 else
 816                         splitopt="  "
 817                 fi
 818         fi
 819
 820
 821 #       if [ $nseq -gt 5000 ]; then
 822 #               fft=0
 823 #       fi
 824         if [ $forcefft -eq 1 ]; then
 825                 param_fft=" -G "
 826                 fft=1
 827         elif [ $fft -eq 1 ]; then
 828                 param_fft=" -F "
 829         else
 830                 param_fft=" "
 831         fi
 832
 833         if [ $seed != "x" -a $seedtable != "x" ]; then
 834                         echo 'Use either one of seedtable and seed.  Not both.' 1>&2
 835                         exit 1
 836         fi
 837
 838         if [ $treein -eq 1 ]; then
 839 #               if [ $iterate -gt 0 ]; then
 840 #                       echo 'Not supported yet.' 1>&2
 841 #                       exit 1
 842 #               fi
 843                 cycle=1
 844         fi
 845
 846         if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
 847                 if [ $distance = "sixtuples" ]; then
 848                         echo 'Not supported.' 1>&2
 849                         echo 'Please add --globalpair, --localpair, --scarnapair,' 1>&2
 850                         echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
 851                         exit 1
 852                 fi
 853         fi
 854
 855         if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
 856                 if [ $distance = "scarna" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
 857                         strategy="X-I"
 858                 elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
 859                         strategy="Q-I"
 860                 fi
 861         elif [ $distance = "fasta" -a $sw -eq 0 ]; then
 862                 strategy="F-I"
 863         elif [ $distance = "fasta" -a $sw -eq 1 ]; then
 864                 strategy="H-I"
 865         elif [ $distance = "blast" ]; then
 866                 strategy="B-I"
 867         elif [ $distance = "global" -o $distance = "distonly" ]; then
 868                 strategy="G-I"
 869         elif [ $distance = "local" ]; then
 870                 strategy="L-I"
 871         elif [ $distance = "localgenaf" ]; then
 872                 strategy="E-I"
 873         elif [ $distance = "globalgenaf" ]; then
 874                 strategy="K-I"
 875         elif [ $fft -eq 1 ]; then
 876                 strategy="FFT-"
 877         else
 878                 strategy="NW-"
 879         fi
 880         strategy=$strategy"NS-"
 881         if [ $iterate -gt 0 ]; then
 882                 strategy=$strategy"i"
 883         elif [ $distance = "parttree" ]; then
 884                 if [ $partdist = "fasta" ]; then
 885                         strategy=$strategy"FastaPartTree-"$cycle
 886                 elif [ $partdist = "localalign" ]; then
 887                         strategy=$strategy"DPPartTree-"$cycle
 888                 else
 889                         strategy=$strategy"PartTree-"$cycle
 890                 fi
 891         else
 892                 strategy=$strategy$cycle
 893         fi
 894
 895         explanation='?'
 896         performance='Not tested.'
 897         if [ $strategy = "F-INS-i" ]; then
 898                 explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
 899                 performance='Most accurate, but very slow'
 900         elif [ $strategy = "L-INS-i" ]; then
 901                 explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
 902                 performance='Probably most accurate, very slow'
 903         elif [ $strategy = "E-INS-i" ]; then
 904                 explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)'
 905                 performance='Suitable for sequences with long unalignable regions, very slow'
 906         elif [ $strategy = "G-INS-i" ]; then
 907                 explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information'
 908                 performance='Suitable for sequences of similar lengths, very slow'
 909         elif [ $strategy = "X-INS-i" ]; then
 910                 explanation='RNA secondary structure information is taken into account.'
 911                 performance='For short RNA sequences only, extremely slow'
 912         elif [ $strategy = "F-INS-1" ]; then
 913                 explanation='Progressive method incorporating LOCAL pairwise alignment information'
 914         elif [ $strategy = "L-INS-1" ]; then
 915                 explanation='Progressive method incorporating LOCAL pairwise alignment information'
 916         elif [ $strategy = "G-INS-1" ]; then
 917                 explanation='Progressive method incorporating GLOBAL pairwise alignment information'
 918         elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then
 919                 explanation='Iterative refinement method (max. '$iterate' iterations)'
 920                 if [ $iterate -gt 2 ]; then
 921                         performance='Accurate but slow'
 922                 else
 923                         performance='Standard'
 924                 fi
 925         elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then
 926                 explanation='Progressive method (guide trees were built '$cycle' times.)'
 927                 performance='Fast but rough'
 928         elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then
 929                 explanation='Progressive method (rough guide tree was used.)'
 930                 performance='Very fast but very rough'
 931         fi
 932
 933         if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
 934                 outputopt=" -c $strategy -r order  "
 935         elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
 936                 outputopt=" -c $strategy  "
 937         elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
 938                 outputopt=" -f -r order "
 939         else
 940                 outputopt="null"
 941         fi
 942
 943         (
 944                 cd $TMPFILE;
 945                 if [ $quiet -gt 0 ]; then
 946                         if [ $seed != "x" ]; then
 947                                 mv infile infile2
 948                                 cat /dev/null > infile
 949                                 cat /dev/null > hat3.seed
 950                                 seedoffset=0
 951 #                               echo "seednseq="$seednseq
 952 #                               echo "seedoffset="$seedoffset
 953                                 set $seednseq > /dev/null
 954 #                               echo $#
 955                                 while [ $# -gt 1 ]
 956                                 do
 957                                         shift
 958 #                                       echo "num="$#
 959                                         "$prefix/multi2hat3s" -t $nseq  -o $seedoffset -i seed$# >> infile 2>/dev/null || exit 1
 960                                         cat hat3 >> hat3.seed
 961 #                                       echo "$1"
 962                                         seedoffset=`expr $seedoffset + $1`
 963 #                                       echo "$1"
 964 #                                       echo "seedoffset="$seedoffset
 965                                 done;
 966 #                               echo "seedoffset="$seedoffset
 967                                 cat infile2 >> infile
 968                         elif [ $seedtable != "x" ]; then
 969                                 cat _seedtablefile > hat3.seed
 970                         else
 971                                 cat /dev/null > hat3.seed
 972                         fi
 973 #                       cat hat3.seed
 974                         if [ $mccaskill -eq 1 ]; then
 975                                 "$prefix/mccaskillwrap" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
 976                         elif [ $contrafold -eq 1 ]; then
 977                                 "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
 978                         fi
 979                         if [ $distance = "fasta" ]; then
 980                                 "$prefix/dndfast7" $swopt < infile > /dev/null  2>&1      || exit 1
 981                                 cat hat3.seed hat3 > hatx
 982                                 mv hatx hat3
 983                                 "$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
 984                         elif [ $distance = "blast" ]; then
 985                                 "$prefix/dndblast" < infile > /dev/null  2>&1      || exit 1
 986                                 cat hat3.seed hat3 > hatx
 987                                 mv hatx hat3
 988                                 "$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
 989                         elif [ $distance = "foldalignlocal" ]; then
 990                                 "$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null  2>&1      || exit 1
 991                                 cat hat3.seed hat3 > hatx
 992                                 mv hatx hat3
 993                                 "$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
 994                         elif [ $distance = "foldalignglobal" ]; then
 995                                 "$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $pgexp -f $pggop -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null  2>&1      || exit 1
 996                                 cat hat3.seed hat3 > hatx
 997                                 mv hatx hat3
 998                                 "$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
 999                         elif [ $distance = "slara" ]; then
1000                                 "$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null  2>&1      || exit 1
1001                                 cat hat3.seed hat3 > hatx
1002                                 mv hatx hat3
1003                                 "$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
1004                         elif [ $distance = "lara" ]; then
1005                                 "$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null  2>&1      || exit 1
1006                                 cat hat3.seed hat3 > hatx
1007                                 mv hatx hat3
1008                                 "$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
1009                         elif [ $distance = "scarna" ]; then
1010                                 "$prefix/pairlocalalign"   $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null  2>&1      || exit 1
1011                                 cat hat3.seed hat3 > hatx
1012                                 mv hatx hat3
1013                                 "$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
1014                         elif [ $distance = "global" ]; then
1015                                 "$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -F < infile > /dev/null  2>&1      || exit 1
1016                                 cat hat3.seed hat3 > hatx
1017                                 mv hatx hat3
1018                                 "$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
1019                         elif [ $distance = "local" ]; then
1020                                 "$prefix/pairlocalalign"   $seqtype $model  -g $lexp -f $lgop  -h $laof -L < infile > /dev/null  2>&1      || exit 1
1021                                 cat hat3.seed hat3 > hatx
1022                                 mv hatx hat3
1023                                 "$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
1024                         elif [ $distance = "globalgenaf" ]; then
1025                                 "$prefix/pairlocalalign"   $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null 2>&1    || exit 1
1026                                 cat hat3.seed hat3 > hatx
1027                                 mv hatx hat3
1028                                 "$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
1029                         elif [ $distance = "localgenaf" ]; then
1030                                 "$prefix/pairlocalalign"   $seqtype $model -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null  2>&1      || exit 1
1031                                 cat hat3.seed hat3 > hatx
1032                                 mv hatx hat3
1033                                 "$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
1034                         elif [ $distance = "distonly" ]; then
1035                                 "$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null  2>&1      || exit 1
1036                                 "$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
1037                         elif [ $distance = "parttree" ]; then
1038                                 "$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre 2>/dev/null || exit 1
1039                                 mv hat3.seed hat3
1040                         else
1041                                 "$prefix/disttbfast" $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $algopt $treealg < infile   > pre 2>/dev/null || exit 1
1042                                 mv hat3.seed hat3
1043                         fi
1044                         while [ $cycle -gt 1 ]
1045                         do
1046                                 if [ $distance = "parttree" ]; then
1047                                         mv pre infile
1048                                         "$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre 2>/dev/null || exit 1
1049                                 else
1050                                         "$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
1051                                 fi
1052                                 cycle=`expr $cycle - 1`
1053                         done
1054                         if [ $iterate -gt 0 ]; then
1055                                 if [ $distance = "sixtuples" ]; then
1056                                     "$prefix/dndpre"       < pre     > /dev/null 2>&1 || exit 1
1057                                 fi
1058                                 "$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
1059                         fi
1060                 else
1061                         if [ $seed != "x" ]; then
1062                                 mv infile infile2
1063                                 cat /dev/null > infile
1064                                 cat /dev/null > hat3.seed
1065                                 seedoffset=0
1066 #                               echo "seednseq="$seednseq
1067 #                               echo "seedoffset="$seedoffset
1068                                 set $seednseq > /dev/null
1069 #                               echo $#
1070                                 while [ $# -gt 1 ]
1071                                 do
1072                                         shift
1073 #                                       echo "num="$#
1074                                         "$prefix/multi2hat3s" -t $nseq  -o $seedoffset -i seed$# >> infile  || exit 1
1075                                         cat hat3 >> hat3.seed
1076 #                                       echo "$1"
1077                                         seedoffset=`expr $seedoffset + $1`
1078 #                                       echo "$1"
1079 #                                       echo "seedoffset="$seedoffset
1080                                 done;
1081 #                               echo "seedoffset="$seedoffset
1082                                 cat infile2 >> infile
1083                         elif [ $seedtable != "x" ]; then
1084                                 cat _seedtablefile > hat3.seed
1085                         else
1086                                 cat /dev/null > hat3.seed
1087                         fi
1088 #                       cat hat3.seed
1089                         if [ $mccaskill -eq 1 ]; then
1090                                 "$prefix/mccaskillwrap" -d "$prefix" -i infile > hat4  || exit 1
1091                         elif [ $contrafold -eq 1 ]; then
1092                                 "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4  || exit 1
1093                         fi
1094                         if [ $distance = "fasta" ]; then
1095                                 "$prefix/dndfast7" $swopt < infile > /dev/null     || exit 1
1096                                 cat hat3.seed hat3 > hatx
1097                                 mv hatx hat3
1098                                 "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
1099                         elif [ $distance = "blast" ]; then
1100                                 "$prefix/dndblast" < infile > /dev/null     || exit 1
1101                                 cat hat3.seed hat3 > hatx
1102                                 mv hatx hat3
1103                                 "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
1104                         elif [ $distance = "foldalignlocal" ]; then
1105                                 "$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null || exit 1
1106                                 cat hat3.seed hat3 > hatx
1107                                 mv hatx hat3
1108                                 "$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
1109                         elif [ $distance = "foldalignglobal" ]; then
1110                                 "$prefix/pairlocalalign" $seqtype $foldalignopt $model -g $pgexp -f $pggop  -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null || exit 1
1111                                 cat hat3.seed hat3 > hatx
1112                                 mv hatx hat3
1113                                 "$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
1114                         elif [ $distance = "slara" ]; then
1115                                 "$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null || exit 1
1116                                 cat hat3.seed hat3 > hatx
1117                                 mv hatx hat3
1118                                 "$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
1119                         elif [ $distance = "lara" ]; then
1120                                 "$prefix/pairlocalalign" -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null || exit 1
1121                                 cat hat3.seed hat3 > hatx
1122                                 mv hatx hat3
1123                                 "$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
1124                         elif [ $distance = "scarna" ]; then
1125                                 "$prefix/pairlocalalign"   $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null   || exit 1
1126                                 cat hat3.seed hat3 > hatx
1127                                 mv hatx hat3
1128                                 "$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
1129                         elif [ $distance = "global" ]; then
1130                                 "$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof   -F  < infile > /dev/null     || exit 1
1131                                 cat hat3.seed hat3 > hatx
1132                                 mv hatx hat3
1133                                 "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
1134                         elif [ $distance = "local" ]; then
1135                                 "$prefix/pairlocalalign"   $seqtype $model  -g $lexp -f $lgop  -h $laof -L  < infile > /dev/null     || exit 1
1136                                 cat hat3.seed hat3 > hatx
1137                                 mv hatx hat3
1138                                 "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
1139                         elif [ $distance = "globalgenaf" ]; then
1140                                 "$prefix/pairlocalalign"   $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null     || exit 1
1141                                 cat hat3.seed hat3 > hatx
1142                                 mv hatx hat3
1143                                 "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
1144                         elif [ $distance = "localgenaf" ]; then
1145                                 "$prefix/pairlocalalign"   $seqtype $model  -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N  < infile > /dev/null     || exit 1
1146                                 cat hat3.seed hat3 > hatx
1147                                 mv hatx hat3
1148                                 "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
1149                         elif [ $distance = "distonly" ]; then
1150                                 "$prefix/pairlocalalign"   $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null            || exit 1
1151                                 "$prefix/tbfast" $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft $localparam  $algopt $treealg < infile   > /dev/null || exit 1
1152                         elif [ $distance = "parttree" ]; then
1153                                 "$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre || exit 1
1154                                 mv hat3.seed hat3
1155                         else
1156                                 "$prefix/disttbfast" $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft  $algopt $treealg < infile   > pre || exit 1
1157                                 mv hat3.seed hat3
1158                         fi
1159
1160                         while [ $cycle -gt 1 ]
1161                         do
1162                                 if [ $distance = "parttree" ]; then
1163                                         mv pre infile
1164                                         "$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile  > pre || exit 1
1165                                 else
1166                                         "$prefix/tbfast" $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model  -f "-"$gop  -h "-"$aof $param_fft $localparam $algopt -J $treealg < pre > /dev/null || exit 1
1167                                 fi
1168                                 cycle=`expr $cycle - 1`
1169                         done
1170                         if [ $iterate -gt 0 ]; then
1171                                 if [ $distance = "sixtuples" ]; then
1172                                 "$prefix/dndpre"       < pre     > /dev/null 2>&1 || exit 1
1173                                 fi
1174                                 "$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
1175                         fi
1176                 fi
1177
1178
1179
1180                 if [ $coreout -eq 1 ]; then
1181                         "$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2
1182                         mv pre2 pre
1183                 fi
1184                 if [ "$outputopt" = "null" ]; then
1185                         cat < pre || exit 1
1186                 else
1187                         "$prefix/f2cl" $outputopt < pre || exit 1
1188                 fi
1189         )
1190
1191         if [ $treeout -eq 1 ]; then
1192                 cp $TMPFILE/infile.tree "$infilename.tree"
1193         fi
1194
1195         if [ $distout -eq 1 ]; then
1196                 cp $TMPFILE/hat2 "$infilename.hat2"
1197         fi
1198
1199         if [ $quiet -eq 0 ]; then
1200                 echo '' 1>&2
1201                 if [ $mccaskill -eq 1 ]; then
1202                         echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>&2
1203                         echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>&2
1204                         echo "incorporated in the iterative alignment process (4)." 1>&2
1205                         echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>&2
1206                         echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>&2
1207                         echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>&2
1208                         echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
1209                         echo "" 1>&2
1210                 elif [ $contrafold -eq 1 ]; then
1211                         echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>&2
1212                         echo "and then incorporated in the iterative alignment process (4)." 1>&2
1213                         echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>&2
1214                         echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
1215                         echo "" 1>&2
1216                 fi
1217                 if [ $distance = "fasta" -o $partdist = "fasta" ]; then
1218                         echo "Pairwise alignments were computed by FASTA" 1>&2
1219                         echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>&2
1220                 fi
1221                 if [ $distance = "blast" ]; then
1222                         echo "Pairwise alignments were computed by BLAST" 1>&2
1223                         echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>&2
1224                 fi
1225                 if [ $distance = "scarna" ]; then
1226                         echo "Pairwise alignments were computed by MXSCARNA" 1>&2
1227                         echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>&2
1228                 fi
1229                 if [ $distance = "lara" -o $distance = "slara" ]; then
1230                         echo "Pairwise alignments were computed by LaRA" 1>&2
1231                         echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>&2
1232                 fi
1233                 if [ $distance = "foldalignlocal" ]; then
1234                         echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>&2
1235                         echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
1236                 fi
1237                 if [ $distance = "foldalignglobal" ]; then
1238                         echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>&2
1239                         echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
1240                 fi
1241                 printf "\n" 1>&2
1242                 echo 'Strategy:' 1>&2
1243                 printf ' '$strategy 1>&2
1244                 echo ' ('$performance')' 1>&2
1245                 echo ' '$explanation 1>&2
1246                 echo '' 1>&2
1247                 echo "If unsure which option to use, try 'mafft --auto input > output'." 1>&2
1248 #               echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>&2
1249                 echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>&2
1250                 echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>&2
1251                 echo '' 1>&2
1252         fi
1253         exit 0;
1254 fi
1255
1256 prog="awk"
1257
1258 tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
1259 if [ -x "$tmpawk" ]; then
1260         prog="$tmpawk"
1261 fi
1262
1263 tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
1264 if [ -x "$tmpawk" ]; then
1265         prog="$tmpawk"
1266 fi
1267
1268 echo "prog="$prog 1>&2
1269
1270 umask 077
1271 export defaultaof
1272 export defaultgop
1273 export defaultfft
1274 export defaultcycle
1275 export defaultiterate
1276 (
1277 $prog '
1278 BEGIN {
1279         prefix = ENVIRON["prefix"];
1280         version = ENVIRON["version"];
1281         myself = ENVIRON["myself"];
1282         defaultgop = ENVIRON["defaultgop"]
1283         defaultaof = ENVIRON["defaultaof"]
1284         defaultfft = ENVIRON["defaultfft"]
1285         defaultcycle = ENVIRON["defaultcycle"]
1286         defaultiterate = ENVIRON["defaultiterate"]
1287         while( 1 )
1288         {
1289                 options = ""
1290                 printf( "\n" ) > "/dev/tty";
1291                 printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
1292                 printf( "\n" )                                                                           > "/dev/tty";
1293                 printf( "   MAFFT %s\n", version )                                                       > "/dev/tty";
1294                 printf( "\n" )                                                                           > "/dev/tty";
1295                 printf( "        Copyright (c) 2009 Kazutaka Katoh\n" )                                  > "/dev/tty";
1296                 printf( "        NAR 30:3059-3066, NAR 33:511-518\n" )                                   > "/dev/tty";
1297                 printf( "        http://align.bmr.kyushu-u.ac.jp/mafft/software/\n" )       > "/dev/tty";
1298                 printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
1299                 printf( "\n" ) > "/dev/tty";
1300
1301                 while( 1 )
1302                 {
1303                         printf( "\n" ) > "/dev/tty";
1304                         printf( "Input file? (fasta format)\n@ " ) > "/dev/tty";
1305                         res = getline < "/dev/tty";
1306                         close( "/dev/tty" )
1307                         if( res == 0 || NF == 0 )
1308                                 continue;
1309                         infile0 = sprintf( "%s", $1 );
1310                         infile = sprintf( "%s", $1 );
1311
1312                         res = getline < infile;
1313                         close( infile );
1314                         if( res == -1 )
1315                                 printf( "%s: No such file.\n\n", infile ) > "/dev/tty";
1316                         else if( res == 0 )
1317                                 printf( "%s: Empty.\n", infile ) > "/dev/tty";
1318                         else
1319                         {
1320                                 printf( "OK. infile = %s\n\n", infile ) > "/dev/tty";
1321                                 break;
1322                         }
1323                 }
1324                 nseq = 0;
1325
1326                 while( 1 )
1327                 {
1328                         printf( "\n" ) > "/dev/tty";
1329                         printf( "Output file?\n" ) > "/dev/tty";
1330                         printf( "@ " ) > "/dev/tty";
1331                         res = getline < "/dev/tty";
1332                         close( "/dev/tty" );
1333                         if( res == 0 || NF == 0 )
1334                                 continue;
1335                         else
1336                         {
1337                                 outfile = sprintf( "%s", $1 );
1338                                 printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
1339                                 break;
1340                         }
1341                 }
1342
1343
1344                 while( 1 )
1345                 {
1346                         retree = defaultcycle
1347                         printf( "\n" ) > "/dev/tty";
1348                         printf( "Number of tree-rebuilding?\n" ) > "/dev/tty";
1349                         printf( "@ [%d] ", retree ) > "/dev/tty";
1350                         res = getline < "/dev/tty";
1351                         close( "/dev/tty" );
1352                         if( res == 0 )
1353                                 continue;
1354                         else if( NF == 0 )
1355                                 ;
1356                         else
1357                                 retree = 0 + $1;
1358                         if( retree < 1 || 10 < retree )
1359                                 ;
1360                         else
1361                         {
1362                                 printf( "OK. %d\n\n", retree ) > "/dev/tty";
1363                                 break;
1364                         }
1365                 }
1366
1367                 while( 1 )
1368                 {
1369                         niterate = defaultiterate;
1370                         printf( "\n" ) > "/dev/tty";
1371                         printf( "Maximum number of iterations?\n" ) > "/dev/tty";
1372                         printf( "@ [%d] ", niterate ) > "/dev/tty";
1373                         res = getline < "/dev/tty";
1374                         close( "/dev/tty" );
1375                         if( res == 0 )
1376                                 continue;
1377                         else if( NF == 0 )
1378                                 ;
1379                         else
1380                                 niterate = 0 + $1;
1381                         if( niterate < 0 || 1000 < niterate )
1382                                 ;
1383                         else
1384                         {
1385                                 printf( "OK. %d\n\n", niterate ) > "/dev/tty";
1386                                 break;
1387                         }
1388                 }
1389
1390                 while( 1 )
1391                 {
1392                         fft = defaultfft;
1393                         printf( "\n" ) > "/dev/tty";
1394                         printf( "Use fft?\n" ) > "/dev/tty";
1395                         printf( "@ [%s] ", fft?"Yes":"No" ) > "/dev/tty";
1396                         res = getline < "/dev/tty";
1397                         close( "/dev/tty" );
1398                         if( res == 0 )
1399                                 continue;
1400                         else if( NF == 0 )
1401                         {
1402                                 break;
1403                         }
1404                         else if( NF == 0 || $0 ~ /^[Yy]/ )
1405                         {
1406                                 fft = 1;
1407                                 break;
1408                         }
1409                         else if( NF == 0 || $0 ~ /^[Nn]/ )
1410                         {
1411                                 fft = 0;
1412                                 break;
1413                         }
1414                 }
1415                 if( fft )
1416                 {
1417                                 printf( "OK. FFT is enabled.\n\n" ) > "/dev/tty";
1418                                 fftparam = " ";
1419                 }
1420                 else
1421                 {
1422                                 printf( "OK. FFT is disabled.\n\n" ) > "/dev/tty";
1423                                 fftparam = " --nofft ";
1424                 }
1425
1426                 while( 1 )
1427                 {
1428                         scoringmatrix = 3;
1429                         printf( "\n" ) > "/dev/tty";
1430                         printf( "Scoring matrix? (ignored when DNA sequence is input.)\n" ) > "/dev/tty";
1431                         printf( " 1. BLOSUM 30\n" ) > "/dev/tty";
1432                         printf( " 2. BLOSUM 45\n" ) > "/dev/tty";
1433                         printf( " 3. BLOSUM 62\n" ) > "/dev/tty";
1434                         printf( " 4. BLOSUM 80\n" ) > "/dev/tty";
1435                         printf( " 5. JTT 200\n" ) > "/dev/tty";
1436                         printf( " 6. JTT 100\n" ) > "/dev/tty";
1437                         printf( "@ [%d] ", scoringmatrix ) > "/dev/tty";
1438                         res = getline < "/dev/tty";
1439                         close( "/dev/tty" );
1440                         if( res == 0 )
1441                                 continue;
1442                         else if( NF == 0 )
1443                                 ;
1444                         else
1445                                 scoringmatrix = 0 + $1;
1446                         if( scoringmatrix < 1 || 6 < scoringmatrix )
1447                                 ;
1448                         else
1449                         {
1450                                 break;
1451                         }
1452                 }
1453                 if( scoringmatrix == 1 )
1454                         scoringparam = " --bl 30 ";
1455                 else if( scoringmatrix == 2 )
1456                         scoringparam = " --bl 45 ";
1457                 else if( scoringmatrix == 3 )
1458                         scoringparam = " --bl 62 ";
1459                 else if( scoringmatrix == 4 )
1460                         scoringparam = " --bl 80 ";
1461                 else if( scoringmatrix == 5 )
1462                         scoringparam = " --jtt 200 ";
1463                 else if( scoringmatrix == 6 )
1464                         scoringparam = " --jtt 100 ";
1465                 printf( "OK. %s\n\n",scoringparam ) > "/dev/tty";
1466
1467                 while( 1 )
1468                 {
1469                         penalty = 0.0 + defaultgop;
1470                         offset = 0.0 + defaultaof;
1471                         printf( "\n" ) > "/dev/tty";
1472                         printf( "Parameters (gap opening penalty, offset)?\n", penalty, offset ) > "/dev/tty";
1473                         printf( "@ [%5.3f, %5.3f] ", penalty, offset ) > "/dev/tty";
1474                         res = getline < "/dev/tty";
1475                         close( "/dev/tty" );
1476                         if( res == 0 )
1477                                 continue;
1478                         else if( NF == 2 )
1479                         {
1480                                 penalty = 0.0 + $1;
1481                                 offset = 0.0 + $2;
1482                         }
1483                         else if( NF == 0 )
1484                                 ;
1485                         else
1486                                 continue;
1487                         if( penalty < 0.0 || 10.0 < penalty )
1488                                 ;
1489                         else if( offset < 0.0 || 10.0 < offset )
1490                                 ;
1491                         else
1492                         {
1493                                 printf( "OK. %5.3f %5.3f\n\n", penalty, offset ) > "/dev/tty";
1494                                 break;
1495                         }
1496                 }
1497
1498                 command = sprintf( "\"%s\" %s --retree %d --maxiterate %d %s --op %f --ep %f %s > %s", myself, fftparam, retree, niterate, scoringparam, penalty, offset, infile, outfile );
1499                 gsub( /\\/, "/", command );
1500
1501
1502                 printf( "%s\n\n", command ) > "/dev/tty";
1503
1504
1505                 while( 1 )
1506                 {
1507                         go = 0;
1508                         printf( "\n" ) > "/dev/tty";
1509                         printf( "OK?\n" ) > "/dev/tty";
1510                         printf( "@ [Y] " ) > "/dev/tty";
1511                         res = getline < "/dev/tty";
1512                         close( "/dev/tty" );
1513                         if( res == 0 )
1514                                 continue;
1515                         else if( NF == 0 || $0 ~ /^[Yy]/ )
1516                         {
1517                                 go=1;
1518                                 break;
1519                         }
1520                         else
1521                                 break;
1522                 }
1523                 if( go ) break;
1524                 printf( "\n" ) > "/dev/tty";
1525                 printf( "\n" ) > "/dev/tty";
1526         }
1527         system( command );
1528         printf( "Press Enter to exit." ) > "/dev/tty";
1529         res = getline < "/dev/tty";
1530 }
1531 '
1532 )
1533 exit 0;