binaries/src/mafft/scripts/mafft

   1 #! /bin/sh
   2
   3
   4 er=0;
   5 myself=`dirname "$0"`/`basename "$0"`; export myself
   6 version="v6.857b (2011/05/30)"; 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 elif [ `echo $os | grep -i linux` ]; then
  17         os="linux"
  18 else
  19         os="unix"
  20 fi
  21 export os
  22
  23 if [ "$MAFFT_BINARIES" ]; then
  24         prefix="$MAFFT_BINARIES"
  25 else
  26         prefix=/usr/local/libexec/mafft
  27 fi
  28 export prefix
  29
  30 if [ $# -gt 0 ]; then
  31         if [ "$1" = "--man" ]; then
  32                 man "$prefix/mafft.1"
  33                 exit 0;
  34         fi
  35 fi
  36
  37 if [ ! -x "$prefix/tbfast" ]; then
  38         echo "" 1>&2
  39         echo "correctly installed?" 1>&2
  40         echo "mafft binaries have to be installed in \$MAFFT_BINARIES" 1>&2
  41         echo "or the $prefix directory". 1>&2
  42         echo "" 1>&2
  43         exit 1
  44         er=1
  45 fi
  46
  47 defaultiterate=0
  48 defaultcycle=2
  49 defaultgop="1.53"
  50 #defaultaof="0.123"
  51 defaultaof="0.000"
  52 defaultlaof="0.100"
  53 defaultlgop="-2.00"
  54 defaultfft=1
  55 defaultrough=0
  56 defaultdistance="sixtuples"
  57 #defaultdistance="local"
  58 defaultweighti="2.7"
  59 defaultweightr="0.0"
  60 defaultweightm="1.0"
  61 defaultmccaskill=0
  62 defaultcontrafold=0
  63 defaultalgopt="  "
  64 defaultalgoptit="  "
  65 defaultsbstmodel=" -b 62 "
  66 defaultfmodel=" "
  67 defaultkappa=" "
  68 if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then
  69         defaultfft=1
  70         defaultcycle=1
  71         defaultiterate=1000
  72         defaultdistance="scarna"
  73         defaultweighti="3.2"
  74         defaultweightr="8.0"
  75         defaultweightm="2.0"
  76         defaultmccaskill=1
  77         defaultcontrafold=0
  78         defaultalgopt=" -A "
  79         defaultalgoptit=" -AB " ## chui
  80         defaultaof="0.0"
  81         defaultsbstmodel=" -b 62 "
  82         defaultkappa=" "
  83         defaultfmodel=" -a "
  84 elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
  85         defaultfft=1
  86         defaultcycle=1
  87         defaultiterate=1000
  88         defaultdistance="global"
  89         defaultweighti="3.2"
  90         defaultweightr="8.0"
  91         defaultweightm="2.0"
  92         defaultmccaskill=1
  93         defaultcontrafold=0
  94         defaultalgopt=" -A "
  95         defaultalgoptit=" -AB " ## chui
  96         defaultaof="0.0"
  97         defaultsbstmodel=" -b 62 "
  98         defaultkappa=" "
  99         defaultfmodel=" -a "
 100 elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
 101         defaultfft=0
 102         defaultcycle=1
 103         defaultiterate=1000
 104         defaultdistance="local"
 105 elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then
 106         defaultfft=1
 107         defaultcycle=1
 108         defaultiterate=1000
 109         defaultdistance="global"
 110 elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then
 111         defaultfft=0
 112         defaultcycle=1
 113         defaultiterate=1000
 114         defaultdistance="localgenaf"
 115 elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
 116         defaultfft=1
 117         defaultcycle=2
 118         defaultdistance="sixtuples"
 119 elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
 120         defaultfft=1
 121         defaultcycle=2
 122         defaultiterate=2
 123         defaultdistance="sixtuples"
 124 elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
 125         defaultfft=0
 126         defaultcycle=2
 127         defaultdistance="sixtuples"
 128 elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
 129         defaultfft=0
 130         defaultcycle=2
 131         defaultiterate=2
 132         defaultdistance="sixtuples"
 133 fi
 134 outputfile=""
 135 namelength=15
 136 anysymbol=0
 137 parallelizationstrategy="BAATARI2"
 138 kappa=$defaultkappa
 139 sbstmodel=$defaultsbstmodel
 140 fmodel=$defaultfmodel
 141 gop=$defaultgop
 142 aof=$defaultaof
 143 cycle=$defaultcycle
 144 iterate=$defaultiterate
 145 fft=$defaultfft
 146 rough=$defaultrough
 147 distance=$defaultdistance
 148 forcefft=0
 149 memopt=" "
 150 weightopt=" "
 151 GGOP="-6.00"
 152 LGOP="-6.00"
 153 LEXP="-0.000"
 154 GEXP="-0.000"
 155 lgop=$defaultlgop
 156 lexp="-0.100"
 157 laof=$defaultlaof
 158 pggop="-2.00"
 159 pgexp="-0.10"
 160 pgaof="0.10"
 161 rgop="-1.530"
 162 rgep="-0.000"
 163 seqtype="  "
 164 weighti=$defaultweighti
 165 weightr=$defaultweightr
 166 weightm=$defaultweightm
 167 rnaalifold=0
 168 mccaskill=$defaultmccaskill
 169 contrafold=$defaultcontrafold
 170 quiet=0
 171 debug=0
 172 sw=0
 173 algopt=$defaultalgopt
 174 algoptit=$defaultalgoptit
 175 scorecalcopt=" "
 176 coreout=0
 177 corethr="0.5"
 178 corewin="100"
 179 coreext=" "
 180 outputformat="pir"
 181 outorder="input"
 182 seed="x"
 183 seedtable="x"
 184 auto=0
 185 groupsize=-1
 186 partsize=50
 187 partdist="sixtuples"
 188 partorderopt=" -x "
 189 treeout=0
 190 distout=0
 191 treein=0
 192 topin=0
 193 treeinopt="  "
 194 seedfiles="/dev/null"
 195 seedtablefile="/dev/null"
 196 aamatrix="/dev/null"
 197 treeinfile="/dev/null"
 198 rnascoremtx=" "
 199 laraparams="/dev/null"
 200 foldalignopt=" "
 201 treealg=" -X "
 202 scoreoutarg=" "
 203 numthreads=0
 204 randomseed=0
 205 addfile="/dev/null"
 206 addarg0=" "
 207 outnum=" "
 208 if [ $# -gt 0 ]; then
 209         while [ $# -gt 1 ];
 210         do
 211                 if [ "$1" = "--auto" ]; then
 212                         auto=1
 213                 elif [ "$1" = "--anysymbol" ]; then
 214                         anysymbol=1
 215                 elif [ "$1" = "--preservecase" ]; then
 216                         anysymbol=1
 217                 elif [ "$1" = "--clustalout" ]; then
 218                         outputformat="clustal"
 219                 elif [ "$1" = "--phylipout" ]; then
 220                         outputformat="phylip"
 221                 elif [ "$1" = "--reorder" ]; then
 222                         outorder="aligned"
 223                         partorderopt=" "
 224                 elif [ "$1" = "--inputorder" ]; then
 225                         outorder="input"
 226                         partorderopt=" -x "
 227                 elif [ "$1" = "--unweight" ]; then
 228                         weightopt=" -u "
 229                 elif [ "$1" = "--algq" ]; then
 230                         algopt=" -Q "
 231                         algoptit=" -QB "
 232                 elif [ "$1" = "--namelength" ]; then
 233                         shift
 234                         namelength=`expr "$1" - 0`
 235                 elif [ "$1" = "--groupsize" ]; then
 236                         shift
 237                         groupsize=`expr "$1" - 0`
 238                 elif [ "$1" = "--partsize" ]; then
 239                         shift
 240                         partsize=`expr "$1" - 0`
 241                 elif [ "$1" = "--parttree" ]; then
 242                         distance="parttree"
 243                         partdist="sixtuples"
 244                 elif [ "$1" = "--dpparttree" ]; then
 245                         distance="parttree"
 246                         partdist="localalign"
 247                 elif [ "$1" = "--fastaparttree" ]; then
 248                         distance="parttree"
 249                         partdist="fasta"
 250                 elif [ "$1" = "--treeout" ]; then
 251                         treeout=1
 252                 elif [ "$1" = "--distout" ]; then
 253                         distout=1
 254                 elif [ "$1" = "--fastswpair" ]; then
 255                         distance="fasta"
 256                         sw=1
 257                 elif [ "$1" = "--fastapair" ]; then
 258                         distance="fasta"
 259                         sw=0
 260                 elif [ "$1" = "--averagelinkage" ]; then
 261                         treealg=" -E "
 262                 elif [ "$1" = "--minimumlinkage" ]; then
 263                         treealg=" -q "
 264                 elif [ "$1" = "--noscore" ]; then
 265                         scorecalcopt=" -Z "
 266                 elif [ "$1" = "--6merpair" ]; then
 267                         distance="sixtuples"
 268                 elif [ "$1" = "--blastpair" ]; then
 269                         distance="blast"
 270                 elif [ "$1" = "--globalpair" ]; then
 271                         distance="global"
 272                 elif [ "$1" = "--localpair" ]; then
 273                         distance="local"
 274                 elif [ "$1" = "--scarnapair" ]; then
 275                         distance="scarna"
 276                 elif [ "$1" = "--larapair" ]; then
 277                         distance="lara"
 278                 elif [ "$1" = "--slarapair" ]; then
 279                         distance="slara"
 280                 elif [ "$1" = "--foldalignpair" ]; then
 281                         distance="foldalignlocal"
 282                 elif [ "$1" = "--foldalignlocalpair" ]; then
 283                         distance="foldalignlocal"
 284                 elif [ "$1" = "--foldalignglobalpair" ]; then
 285                         distance="foldalignglobal"
 286                 elif [ "$1" = "--globalgenafpair" ]; then
 287                         distance="globalgenaf"
 288                 elif [ "$1" = "--localgenafpair" ]; then
 289                         distance="localgenaf"
 290                 elif [ "$1" = "--genafpair" ]; then
 291                         distance="localgenaf"
 292                 elif [ "$1" = "--memsave" ]; then
 293                         memopt=" -M -B "         # -B (bunkatsunashi no riyu ga omoidasenai)
 294                 elif [ "$1" = "--nomemsave" ]; then
 295                         memopt=" -N "
 296                 elif [ "$1" = "--nuc" ]; then
 297                         seqtype=" -D "
 298                 elif [ "$1" = "--amino" ]; then
 299                         seqtype=" -P "
 300                 elif [ "$1" = "--fft" ]; then
 301                         fft=1
 302                         forcefft=1
 303                 elif [ "$1" = "--nofft" ]; then
 304                         fft=0
 305                 elif [ "$1" = "--quiet" ]; then
 306                         quiet=1
 307                 elif [ "$1" = "--debug" ]; then
 308                         debug=1
 309                 elif [ "$1" = "--coreext" ]; then
 310                         coreext=" -c "
 311                 elif [ "$1" = "--core" ]; then
 312                         coreout=1
 313                 elif [ "$1" = "--out" ]; then
 314                         shift
 315                         outputfile="$1"
 316                 elif [ "$1" = "--thread" ]; then
 317                         shift
 318                         numthreads=`expr "$1" - 0`
 319                 elif [ "$1" = "--randomseed" ]; then
 320                         shift
 321                         randomseed=`expr "$1" - 0`
 322                 elif [ "$1" = "--bestfirst" ]; then
 323                         parallelizationstrategy="BESTFIRST"
 324                 elif [ "$1" = "--adhoc0" ]; then
 325                         parallelizationstrategy="BAATARI0"
 326                 elif [ "$1" = "--adhoc1" ]; then
 327                         parallelizationstrategy="BAATARI1"
 328                 elif [ "$1" = "--adhoc2" ]; then
 329                         parallelizationstrategy="BAATARI2"
 330                 elif [ "$1" = "--simplehillclimbing" ]; then
 331                         parallelizationstrategy="BAATARI2"
 332                 elif [ "$1" = "--scoreout" ]; then
 333                         scoreoutarg="-S -B"
 334                 elif [ "$1" = "--outnum" ]; then
 335                         scoreoutarg="-n"
 336                 elif [ "$1" = "--addprofile" ]; then
 337                         shift
 338                         addarg0="-I"
 339                         addfile="$1"
 340                 elif [ "$1" = "--add" ]; then
 341                         shift
 342                         addarg0="-K -I"
 343                         addfile="$1"
 344                 elif [ "$1" = "--maxiterate" ]; then
 345                         shift
 346                         iterate=`expr "$1" - 0`
 347                 elif [ "$1" = "--retree" ]; then
 348                         shift
 349                         cycle=`expr "$1" - 0`
 350                 elif [ "$1" = "--aamatrix" ]; then
 351                         shift
 352                         sbstmodel=" -b -1 "
 353                         aamatrix="$1"
 354                 elif [ "$1" = "--treein" ]; then
 355                         shift
 356                         treeinopt=" -U "
 357                         treein=1
 358                         treeinfile="$1"
 359                 elif [ "$1" = "--topin" ]; then
 360                         shift
 361                         treeinopt=" -V "
 362                         treein=1
 363                         treeinfile="$1"
 364                         echo "The --topin option has been disabled." 1>&2
 365                         echo "There was a bug in version < 6.530."   1>&2
 366                         echo "This bug has not yet been fixed."      1>&2
 367                         exit 1
 368                 elif [ "$1" = "--kappa" ]; then
 369                         shift
 370                         kappa=" -k $1 "
 371                 elif [ "$1" = "--fmodel" ]; then
 372                         fmodel=" -a "
 373                 elif [ "$1" = "--jtt" ]; then
 374                         shift
 375                         sbstmodel=" -j $1"
 376                 elif [ "$1" = "--kimura" ]; then
 377                         shift
 378                         sbstmodel=" -j $1"
 379                 elif [ "$1" = "--tm" ]; then
 380                         shift
 381                         sbstmodel=" -m $1"
 382                 elif [ "$1" = "--bl" ]; then
 383                         shift
 384                         sbstmodel=" -b $1"
 385                 elif [ "$1" = "--weighti" ]; then
 386                         shift
 387                         weighti="$1"
 388                 elif [ "$1" = "--weightr" ]; then
 389                         shift
 390                         weightr="$1"
 391                 elif [ "$1" = "--weightm" ]; then
 392                         shift
 393                         weightm="$1"
 394                 elif [ "$1" = "--rnaalifold" ]; then
 395                         rnaalifold=1
 396                 elif [ "$1" = "--mccaskill" ]; then
 397                         mccaskill=1
 398                         contrafold=0
 399                 elif [ "$1" = "--contrafold" ]; then
 400                         mccaskill=0
 401                         contrafold=1
 402                 elif [ "$1" = "--ribosum" ]; then
 403                         rnascoremtx=" -s "
 404                 elif [ "$1" = "--op" ]; then
 405                         shift
 406                         gop="$1"
 407                 elif [ "$1" = "--ep" ]; then
 408                         shift
 409                         aof="$1"
 410                 elif [ "$1" = "--rop" ]; then
 411                         shift
 412                         rgop="$1"
 413                 elif [ "$1" = "--rep" ]; then
 414                         shift
 415                         rgep="$1"
 416                 elif [ "$1" = "--lop" ]; then
 417                         shift
 418                         lgop="$1"
 419                 elif [ "$1" = "--LOP" ]; then
 420                         shift
 421                         LGOP="$1"
 422                 elif [ "$1" = "--lep" ]; then
 423                         shift
 424                         laof="$1"
 425                 elif [ "$1" = "--lexp" ]; then
 426                         shift
 427                         lexp="$1"
 428                 elif [ "$1" = "--LEXP" ]; then
 429                         shift
 430                         LEXP="$1"
 431                 elif [ "$1" = "--GEXP" ]; then
 432                         shift
 433                         GEXP="$1"
 434                 elif [ "$1" = "--GOP" ]; then
 435                         shift
 436                         GGOP="$1"
 437                 elif [ "$1" = "--gop" ]; then
 438                         shift
 439                         pggop="$1"
 440                 elif [ "$1" = "--gep" ]; then
 441                         shift
 442                         pgaof="$1"
 443                 elif [ "$1" = "--gexp" ]; then
 444                         shift
 445                         pgexp="$1"
 446                 elif [ "$1" = "--laraparams" ]; then
 447                         shift
 448                         laraparams="$1"
 449                 elif [ "$1" = "--corethr" ]; then
 450                         shift
 451                         corethr="$1"
 452                 elif [ "$1" = "--corewin" ]; then
 453                         shift
 454                         corewin="$1"
 455                 elif [ "$1" = "--seedtable" ]; then
 456                         shift
 457                         seedtable="y"
 458                         seedtablefile="$1"
 459                 elif [ "$1" = "--seed" ]; then
 460                         shift
 461                         seed="m"
 462                         seedfiles="$seedfiles $1"
 463                 elif [ $progname = "fftns" -o  $progname = "nwns" ]; then
 464                         if [ "$1" -gt 0 ]; then
 465                                 cycle=`expr "$1" - 0`
 466                         fi
 467                 else
 468                         echo "Unknown option:  $1" 1>&2
 469                         er=1;
 470                 fi
 471                 shift
 472         done;
 473
 474
 475
 476 #       TMPFILE=/tmp/$progname.$$
 477         TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`
 478         if [ $? -ne 0 ]; then
 479                 echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
 480                 TMPFILE=`mktemp -d /tmp/$progname.XXXXXXXXXX`
 481         fi
 482         umask 077
 483 #       mkdir  $TMPFILE  || er=1
 484         if [ $debug -eq 1 ]; then
 485                 trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0
 486         else
 487                 trap "rm -rf $TMPFILE " 0
 488         fi
 489         if [ $# -eq 1 ]; then
 490                 if [ -r "$1" -o "$1" = - ]; then
 491
 492                         if [ -r "$addfile" ]; then
 493                                 printf '';
 494                         else
 495                                 echo "$0": Cannot open "$addfile". 1>&2
 496                                 exit 1;
 497                         fi
 498
 499                         cat "$1"              | tr "\r" "\n" > $TMPFILE/infile
 500                         echo ""                             >> $TMPFILE/infile
 501                         cat "$addfile"        | tr "\r" "\n" | grep -v "^$" >> $TMPFILE/infile
 502                         cat "$addfile"        | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_addfile
 503                         cat "$aamatrix"       | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_aamtx
 504                         cat "$treeinfile"     | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_guidetree
 505                         cat "$seedtablefile"  | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_seedtablefile
 506                         cat "$laraparams"     | tr "\r" "\n" | grep -v "^$" > $TMPFILE/_lara.params
 507 #                       echo $seedfiles
 508                         infilename="$1"
 509                         seedfilesintmp="/dev/null"
 510                         seednseq="0"
 511                         set $seedfiles > /dev/null
 512                         while [ $# -gt 1 ];
 513                         do
 514                                 shift
 515                                 if [ -r "$1" ]; then
 516                                         cat "$1" | tr "\r" "\n" >  $TMPFILE/seed$#
 517                                 else
 518                                         echo "$0": Cannot open "$1". 1>&2
 519                                         exit 1;
 520                                 fi
 521                                 seednseq=$seednseq" "`grep -c '^[>|=]' $TMPFILE/seed$#`
 522                                 seedfilesintmp=$seedfilesintmp" "seed$#
 523                         done
 524 #                       ls $TMPFILE
 525 #                       echo $seedfilesintmp
 526 #                       echo $seednseq
 527
 528
 529                 else
 530                         echo "$0": Cannot open "$1". 1>&2
 531                         er=1
 532 #                       exit 1;
 533                 fi
 534         else
 535                 echo '$#'"=$#" 1>&2
 536                 er=1
 537         fi
 538
 539
 540         if [ $os != "linux" ]; then
 541                 numthreads=0
 542         fi
 543
 544         if [ $numthreads -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
 545                 echo 'Impossible' 1>&2;
 546                 exit 1;
 547         fi
 548
 549         if [ $auto -eq 1 ]; then
 550                 "$prefix/countlen" < $TMPFILE/infile > $TMPFILE/size
 551                 nseq=`awk '{print $1}' $TMPFILE/size`
 552                 nlen=`awk '{print $3}' $TMPFILE/size`
 553                 if [ $nlen -lt 2000 -a $nseq -lt 100 ]; then
 554                         distance="local"
 555                         iterate=1000
 556                 elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
 557                         distance="sixtuples"
 558                         iterate=2
 559                 else
 560                         distance="sixtuples"
 561                         iterate=0
 562                 fi
 563                 if [ $quiet -eq 0 ]; then
 564                         echo "nseq = " $nseq              1>&2
 565                         echo "nlen = " $nlen              1>&2
 566                         echo "distance = " $distance      1>&2
 567                         echo "iterate = " $iterate        1>&2
 568                 fi
 569         fi
 570
 571         if [ $parallelizationstrategy = "BESTFIRST" -o  $parallelizationstrategy = "BAATARI0" ]; then
 572                 iteratelimit=254
 573         else
 574                 iteratelimit=16
 575         fi
 576         if [ $iterate -gt $iteratelimit ]; then    #??
 577                 iterate=$iteratelimit
 578         fi
 579
 580         if [ $rnaalifold -eq 1 ]; then
 581                 rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx "
 582 #               rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R "
 583                 rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R "
 584         elif [ $mccaskill -eq 1 -o $contrafold -eq 1 ]; then
 585                 rnaopt=" -o $rgop -c $weightm -r $weightr "
 586 #               rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx "
 587                 rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx "
 588         else
 589                 rnaopt="  "
 590                 rnaoptit=" -F "
 591         fi
 592
 593         model="$sbstmodel $kappa $fmodel"
 594
 595         if [ $er -eq 1 ]; then
 596                 echo "------------------------------------------------------------------------------" 1>&2
 597                 echo "  MAFFT" $version 1>&2
 598 #               echo "" 1>&2
 599 #               echo "  Input format: fasta" 1>&2
 600 #               echo ""  1>&2
 601 #               echo "  Usage: `basename $0` [options] inputfile > outputfile" 1>&2
 602             echo "  http://mafft.cbrc.jp/alignment/software/" 1>&2
 603                 echo "  NAR 30:3059-3066 (2002), Briefings in Bioinformatics 9:286-298 (2008)"        1>&2
 604 #               echo "------------------------------------------------------------------------------" 1>&2
 605 #               echo "  % mafft in > out" 1>&2
 606                 echo "------------------------------------------------------------------------------" 1>&2
 607 #               echo ""  1>&2
 608                 echo "High speed:" 1>&2
 609                 echo "  % mafft in > out" 1>&2
 610                 echo "  % mafft --retree 1 in > out (fast)" 1>&2
 611                 echo "" 1>&2
 612                 echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2
 613                 echo "  % mafft --maxiterate 1000 --localpair  in > out (% linsi in > out is also ok)" 1>&2
 614                 echo "  % mafft --maxiterate 1000 --genafpair  in > out (% einsi in > out)" 1>&2
 615                 echo "  % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2
 616                 echo "" 1>&2
 617                 echo "If unsure which option to use:" 1>&2
 618                 echo "  % mafft --auto in > out" 1>&2
 619                 echo "" 1>&2
 620 #               echo "Other options:" 1>&2
 621                 echo "--op # :         Gap opening penalty, default: 1.53" 1>&2
 622                 echo "--ep # :         Offset (works like gap extension penalty), default: 0.0" 1>&2
 623                 echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 1>&2
 624                 echo "--clustalout :   Output: clustal format, default: fasta" 1>&2
 625                 echo "--reorder :      Outorder: aligned, default: input order" 1>&2
 626                 echo "--quiet :        Do not report progress" 1>&2
 627                 echo "--thread # :     Number of threads. (# must be <= number of physical cores - 1)" 1>&2
 628 #               echo "" 1>&2
 629 #               echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2
 630 #               echo " most accurate in many cases, assumes only one alignable domain" 1>&2
 631 #               echo "" 1>&2
 632 #               echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2
 633 #               echo " works well if many unalignable residues exist between alignable domains" 1>&2
 634 #               echo "" 1>&2
 635 #               echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2
 636 #               echo " suitable for globally alignable sequences            " 1>&2
 637 #               echo "" 1>&2
 638 #               echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2
 639 #               echo " accurate and slow, iterative refinement method      " 1>&2
 640 #               echo "" 1>&2
 641 #               echo "If the input sequences are long (~1,000,000nt)," 1>&2
 642 #               echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2
 643 #               echo "" 1>&2
 644 #               echo "If many (~5,000) sequences are to be aligned," 1>&2
 645 #               echo "" 1>&2
 646 #               echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2
 647 #               echo "" 1>&2
 648 #               echo " --localpair :      All pairwise local alignment information is included"  1>&2
 649 #               echo "                    to the objective function, default: off"  1>&2
 650 #               echo " --globalpair :     All pairwise global alignment information is included"  1>&2
 651 #               echo "                    to the objective function, default: off"  1>&2
 652 #               echo " --op # :           Gap opening penalty, default: $defaultgop " 1>&2
 653 #               echo " --ep # :           Offset (works like gap extension penalty), default: $defaultaof " 1>&2
 654 #               echo " --bl #, --jtt # :  Scoring matrix, default: BLOSUM62" 1>&2
 655 #               echo "                    Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2
 656 #               echo "                    or JTT (--jtt) # PAM. " 1>&2
 657 #               echo " --nuc or --amino : Sequence type, default: auto" 1>&2
 658 #               echo " --retree # :       The number of tree building in progressive method " 1>&2
 659 #               echo "                    (see the paper for detail), default: $defaultcycle " 1>&2
 660 #               echo " --maxiterate # :   Maximum number of iterative refinement, default: $defaultiterate " 1>&2
 661 #               if [ $defaultfft -eq 1 ]; then
 662 #                       echo " --fft or --nofft:  FFT is enabled or disabled, default: enabled" 1>&2
 663 #               else
 664 #                       echo " --fft or --nofft:  FFT is enabled or disabled, default: disabled" 1>&2
 665 #               fi
 666 #               echo " --memsave:         Memory saving mode" 1>&2
 667 #               echo "                    (for long genomic sequences), default: off" 1>&2
 668 #               echo " --clustalout :     Output: clustal format, default: fasta" 1>&2
 669 #               echo " --reorder :        Outorder: aligned, default: input order" 1>&2
 670 #               echo " --quiet :          Do not report progress" 1>&2
 671 #               echo "-----------------------------------------------------------------------------" 1>&2
 672                 exit 1;
 673         fi
 674         if [ $sw -eq 1 ]; then
 675                 swopt=" -A "
 676         else
 677                 swopt=" "
 678         fi
 679
 680         if [ $distance = "fasta" -o $partdist = "fasta" ]; then
 681                 if [ ! "$FASTA_4_MAFFT" ]; then
 682                         FASTA_4_MAFFT=`which fasta34`
 683                 fi
 684
 685                 if [ ! -x "$FASTA_4_MAFFT" ]; then
 686                         echo ""       1>&2
 687                         echo "== Install FASTA ========================================================" 1>&2
 688                         echo "This option requires the fasta34 program (FASTA version x.xx or higher)"   1>&2
 689                         echo "installed in your PATH.  If you have the fasta34 program but have renamed" 1>&2
 690                         echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2
 691                         echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2
 692                         echo "=========================================================================" 1>&2
 693                         echo "" 1>&2
 694                         exit 1
 695                 fi
 696         fi
 697         if [ $distance = "lara" -o $distance = "slara" ]; then
 698                 if [ ! -x "$prefix/mafft_lara" ]; then
 699                         echo ""       1>&2
 700                         echo "== Install LaRA =========================================================" 1>&2
 701                         echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)."     1>&2
 702                         echo "The executable have to be renamed to 'mafft_lara' and installed into "     1>&2
 703                         echo "the $prefix directory. "                                                   1>&2
 704                         echo "A configuration file of LaRA also have to be given"                        1>&2
 705                         echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
 706                         echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
 707                         echo "=========================================================================" 1>&2
 708                         echo "" 1>&2
 709                         exit 1
 710                 fi
 711                 if [ ! -s "$laraparams" ]; then
 712                         echo ""       1>&2
 713                         echo "== Configure LaRA =======================================================" 1>&2
 714                         echo "A configuration file of LaRA have to be given"                             1>&2
 715                         echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
 716                         echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
 717                         echo "=========================================================================" 1>&2
 718                         echo "" 1>&2
 719                         exit 1
 720                 fi
 721         fi
 722         if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
 723         if [ ! -x "$prefix/foldalign210" ]; then
 724                         echo ""       1>&2
 725                         echo "== Install FOLDALIGN ====================================================" 1>&2
 726                         echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2
 727                         echo "The executable have to be renamed to 'foldalign210' and installed into "   1>&2
 728                         echo "the $prefix directory. "                                                   1>&2
 729                         echo "=========================================================================" 1>&2
 730                         echo "" 1>&2
 731                         exit 1
 732                 fi
 733         fi
 734         if [ $distance = "scarna" ]; then
 735                 if [ ! -x "$prefix/mxscarnamod" ]; then
 736                         echo ""       1>&2
 737                         echo "== Install MXSCARNA ======================================================" 1>&2
 738                         echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required."          1>&2
 739                         echo "Please 'make' at the 'extensions' directory of the MAFFT source package,"   1>&2
 740                         echo "which contains the modified version of MXSCARNA."                           1>&2
 741                         echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html "                1>&2
 742                         echo "==========================================================================" 1>&2
 743                         echo "" 1>&2
 744                         exit 1
 745                 fi
 746         fi
 747         if [ $mccaskill -eq 1 ]; then
 748                 if [ ! -x "$prefix/mxscarnamod" ]; then
 749                         echo ""       1>&2
 750                         echo "== Install MXSCARNA ======================================================" 1>&2
 751                         echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required."          1>&2
 752                         echo "Please 'make' at the 'extensions' directory of the MAFFT source package,"   1>&2
 753                         echo "which contains the modified version of MXSCARNA."                           1>&2
 754                         echo "http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html "                1>&2
 755                         echo "==========================================================================" 1>&2
 756                         echo "" 1>&2
 757                         exit 1
 758                 fi
 759         fi
 760         if [ $contrafold -eq 1 ]; then
 761                 if [ ! -x "$prefix/contrafold" ]; then
 762                         echo ""       1>&2
 763                         echo "== Install CONTRAfold ===================================================" 1>&2
 764                         echo "This option requires CONTRAfold"                                           1>&2
 765                         echo "(Do et al. http://contra.stanford.edu/contrafold/)."                       1>&2
 766                         echo "The executable 'contrafold' have to be installed into "                    1>&2
 767                         echo "the $prefix directory. "                                                   1>&2
 768                         echo "=========================================================================" 1>&2
 769                         echo "" 1>&2
 770                         exit 1
 771                 fi
 772         fi
 773
 774 #old
 775 #       if [ $treeout -eq 1 ]; then
 776 #               parttreeoutopt="-t"
 777 #               if [ $cycle -eq 0 ]; then
 778 #                       treeoutopt="-t -T"
 779 #                       groupsize=1
 780 #                       iterate=0
 781 #                       if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
 782 #                               distance="distonly"
 783 #                       fi
 784 #               else
 785 #                       treeoutopt="-t"
 786 #               fi
 787 #       else
 788 #               parttreeoutopt=" "
 789 #               if [ $cycle -eq 0 ]; then
 790 #                       treeoutopt="-t -T"
 791 #                       iterate=0
 792 #                       if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
 793 #                               distance="distonly"
 794 #                       fi
 795 #               else
 796 #                       treeoutopt=" "
 797 #               fi
 798 #       fi
 799
 800 #new
 801         if [ $cycle -eq 0 ]; then
 802                 treeoutopt="-t -T"
 803                 iterate=0
 804                 if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
 805                         distance="distonly"
 806                 fi
 807                 if [ $treeout -eq 1 ]; then
 808                         parttreeoutopt="-t"
 809                         groupsize=1
 810                 else
 811                         parttreeoutopt=" "
 812                 fi
 813                 if [ $distout -eq 1 ]; then
 814                         distoutopt="-y -T"
 815                 fi
 816         else
 817                 if [ $treeout -eq 1 ]; then
 818                         parttreeoutopt="-t"
 819                         treeoutopt="-t"
 820                 else
 821                         parttreeoutopt=" "
 822                         treeoutopt=" "
 823                 fi
 824                 if [ $distout -eq 1 ]; then
 825                         distoutopt="-y"
 826                 fi
 827         fi
 828 #
 829
 830         formatcheck=`grep -c '^[[:blank:]]\+>' $TMPFILE/infile | head -1 `
 831         if [ $formatcheck -gt 0 ]; then
 832                 echo "The first character of a description line must be " 1>&2
 833                 echo "the greater-than (>) symbol, not a blank."           1>&2
 834                 echo "Please check the format around the following line(s):"  1>&2
 835                 grep -n '^[[:blank:]]\+>' $TMPFILE/infile  1>&2
 836                 exit 1
 837         fi
 838
 839         nseq=`grep -c '^[>|=]' $TMPFILE/infile | head -1 `
 840         if [ $nseq -eq 2 ]; then
 841                 cycle=1
 842         fi
 843         if [ $cycle -gt 3 ]; then
 844                 cycle=3
 845         fi
 846
 847         if [ $nseq -gt 4000 -a $iterate -gt 1 ]; then
 848                 echo "Too many sequences to perform iterative refinement!" 1>&2
 849                 echo "Please use a progressive method." 1>&2
 850                 exit 1
 851         fi
 852
 853
 854         if [ $distance = "sixtuples" -a \( $seed = "x" -a $seedtable = "x" \) ]; then
 855                 localparam=" "
 856         elif [ $distance = "sixtuples" -a \( $seed != "x" -o $seedtable != "x" \) ]; then
 857                 if [ $cycle -lt 2 ]; then
 858                         cycle=2                # nazeda
 859                 fi
 860                 if [ $iterate -lt 2 ]; then
 861                         echo "############################################################################" 1>&2
 862                         echo "# Warning:" 1>&2
 863                         echo "#   Progressive alignment method is incompatible with the --seed option." 1>&2
 864                         echo "#   Automatically switched to the iterative refinement method." 1>&2
 865                         echo "#   " 1>&2
 866                         echo "# Also consider using the '--add' option, which is compatible with" 1>&2
 867                         echo "#   the progressive method and FASTER than the '--seed' option." 1>&2
 868                         echo "#   Usage is:" 1>&2
 869                         echo "#   % mafft --add newSequences existingAlignment > output" 1>&2
 870                         echo "############################################################################" 1>&2
 871                         iterate=2
 872                 fi
 873                 localparam="-l "$weighti
 874         elif [ $distance = "parttree" ]; then
 875                 localparam=" "
 876                 if [ $groupsize -gt -1 ]; then
 877                         cycle=1
 878                 fi
 879         else
 880                 localparam=" -l "$weighti
 881                 if [ $cycle -gt 1 ]; then  # 09/01/08
 882                         cycle=1
 883                 fi
 884         fi
 885
 886         if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
 887                 aof="0.000"
 888         fi
 889
 890         if [ "$memopt" = " -M -B " -a "$distance" != "sixtuples" ]; then
 891                 echo "Impossible" 1>&2
 892                 exit 1
 893         fi
 894 #exit
 895
 896         if [ $distance = "parttree" ]; then
 897                 if [ $seed != "x" -o $seedtable != "x" ]; then
 898                         echo "Impossible" 1>&2
 899                         exit 1
 900                 fi
 901                 if [ $iterate -gt 1 ]; then
 902                         echo "Impossible" 1>&2
 903                         exit 1
 904                 fi
 905                 if [ $outorder = "aligned" ]; then
 906                         outorder="input"
 907                 fi
 908                 outorder="input"   # partorder ga kiku
 909                 if [ $partdist = "localalign" ]; then
 910                         splitopt=" -L "    # -L -l -> fast
 911                 elif [ $partdist = "fasta" ]; then
 912                         splitopt=" -S "
 913                 else
 914                         splitopt="  "
 915                 fi
 916         fi
 917
 918
 919 #       if [ $nseq -gt 5000 ]; then
 920 #               fft=0
 921 #       fi
 922         if [ $forcefft -eq 1 ]; then
 923                 param_fft=" -G "
 924                 fft=1
 925         elif [ $fft -eq 1 ]; then
 926                 param_fft=" -F "
 927         else
 928                 param_fft=" "
 929         fi
 930
 931         if [ $seed != "x" -a $seedtable != "x" ]; then
 932                         echo 'Use either one of seedtable and seed.  Not both.' 1>&2
 933                         exit 1
 934         fi
 935 #       if [ $seedtable != "x" -a $anysymbol -gt 0 ]; then
 936 #                       echo 'The combination of --seedtable and --anysymbol is not supported.' 1>&2
 937 #                       exit 1
 938 #       fi
 939
 940         if [ $treein -eq 1 ]; then
 941 #               if [ $iterate -gt 0 ]; then
 942 #                       echo 'Not supported yet.' 1>&2
 943 #                       exit 1
 944 #               fi
 945                 cycle=1
 946         fi
 947
 948         if [ "$addarg0" != " " ]; then
 949                 "$prefix/countlen" < $TMPFILE/_addfile > $TMPFILE/addsize
 950                 nadd=`awk '{print $1}' $TMPFILE/addsize`
 951                 if [ $nadd -eq "0" ]; then
 952                         echo Check $addfile 1>&2
 953                         exit 1;
 954                 fi
 955                 addarg="$addarg0 $nadd"
 956                 cycle=1
 957                 iterate=0
 958                 if [ $seed != "x" -o $seedtable != "x" ]; then
 959                         echo 'Impossible' 1>&2;
 960                         echo 'Use either ONE of --seed, --seedtable, --addprofile and --add.' 1>&2
 961                         exit 1;
 962                 fi
 963         fi
 964
 965         if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
 966                 if [ $distance = "sixtuples" ]; then
 967                         echo 'Not supported.' 1>&2
 968                         echo 'Please add --globalpair, --localpair, --scarnapair,' 1>&2
 969                         echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
 970                         exit 1
 971                 fi
 972         fi
 973
 974         if [ $mccaskill -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
 975                 if [ $distance = "scarna" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
 976                         strategy="X-I"
 977                 elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
 978                         strategy="Q-I"
 979                 fi
 980         elif [ $distance = "fasta" -a $sw -eq 0 ]; then
 981                 strategy="F-I"
 982         elif [ $distance = "fasta" -a $sw -eq 1 ]; then
 983                 strategy="H-I"
 984         elif [ $distance = "blast" ]; then
 985                 strategy="B-I"
 986         elif [ $distance = "global" -o $distance = "distonly" ]; then
 987                 strategy="G-I"
 988         elif [ $distance = "local" ]; then
 989                 strategy="L-I"
 990         elif [ $distance = "localgenaf" ]; then
 991                 strategy="E-I"
 992         elif [ $distance = "globalgenaf" ]; then
 993                 strategy="K-I"
 994         elif [ $fft -eq 1 ]; then
 995                 strategy="FFT-"
 996         else
 997                 strategy="NW-"
 998         fi
 999         strategy=$strategy"NS-"
1000         if [ $iterate -gt 0 ]; then
1001                 strategy=$strategy"i"
1002         elif [ $distance = "parttree" ]; then
1003                 if [ $partdist = "fasta" ]; then
1004                         strategy=$strategy"FastaPartTree-"$cycle
1005                 elif [ $partdist = "localalign" ]; then
1006                         strategy=$strategy"DPPartTree-"$cycle
1007                 else
1008                         strategy=$strategy"PartTree-"$cycle
1009                 fi
1010         else
1011                 strategy=$strategy$cycle
1012         fi
1013
1014         explanation='?'
1015         performance='Not tested.'
1016         if [ $strategy = "F-INS-i" ]; then
1017                 explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
1018                 performance='Most accurate, but very slow'
1019         elif [ $strategy = "L-INS-i" ]; then
1020                 explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
1021                 performance='Probably most accurate, very slow'
1022         elif [ $strategy = "E-INS-i" ]; then
1023                 explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)'
1024                 performance='Suitable for sequences with long unalignable regions, very slow'
1025         elif [ $strategy = "G-INS-i" ]; then
1026                 explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information'
1027                 performance='Suitable for sequences of similar lengths, very slow'
1028         elif [ $strategy = "X-INS-i" ]; then
1029                 explanation='RNA secondary structure information is taken into account.'
1030                 performance='For short RNA sequences only, extremely slow'
1031         elif [ $strategy = "F-INS-1" ]; then
1032                 explanation='Progressive method incorporating LOCAL pairwise alignment information'
1033         elif [ $strategy = "L-INS-1" ]; then
1034                 explanation='Progressive method incorporating LOCAL pairwise alignment information'
1035         elif [ $strategy = "G-INS-1" ]; then
1036                 explanation='Progressive method incorporating GLOBAL pairwise alignment information'
1037         elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then
1038                 explanation='Iterative refinement method (max. '$iterate' iterations)'
1039                 if [ $iterate -gt 2 ]; then
1040                         performance='Accurate but slow'
1041                 else
1042                         performance='Standard'
1043                 fi
1044         elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then
1045                 explanation='Progressive method (guide trees were built '$cycle' times.)'
1046                 performance='Fast but rough'
1047         elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then
1048                 explanation='Progressive method (rough guide tree was used.)'
1049                 performance='Very fast but very rough'
1050         fi
1051
1052         if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
1053                 outputopt=" -c $strategy -r $TMPFILE/order  "
1054         elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
1055                 outputopt=" -c $strategy  "
1056         elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then
1057                 outputopt=" -y -r $TMPFILE/order "
1058         elif [ $outputformat = "phylip" -a $outorder = "input" ]; then
1059                 outputopt=" -y "
1060         elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
1061                 outputopt=" -f -r $TMPFILE/order "
1062         else
1063                 outputopt="null"
1064         fi
1065
1066         (
1067                 cd $TMPFILE;
1068
1069                 if [ $quiet -gt 0 ]; then
1070
1071                         if [ $anysymbol -eq 1 ]; then
1072                                 mv infile orig
1073                                 "$prefix/replaceu" -i orig > infile 2>/dev/null || exit 1
1074                         fi
1075
1076                         if [ $seed != "x" ]; then
1077                                 mv infile infile2
1078                                 if [ $anysymbol -eq 1 ]; then
1079                                         mv orig orig2
1080                                         cat /dev/null > orig
1081                                 fi
1082                                 cat /dev/null > infile
1083                                 cat /dev/null > hat3.seed
1084                                 seedoffset=0
1085 #                               echo "seednseq="$seednseq
1086 #                               echo "seedoffset="$seedoffset
1087                                 set $seednseq > /dev/null
1088 #                               echo $#
1089                                 while [ $# -gt 1 ]
1090                                 do
1091                                         shift
1092 #                                       echo "num="$#
1093
1094                                         if [ $anysymbol -eq 1 ]; then
1095                                                 cat seed$# >> orig
1096                                                 "$prefix/replaceu" -i seed$# -o $seedoffset > clean 2>/dev/null || exit 1
1097                                                 mv clean seed$#
1098                                         fi
1099                                         "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>/dev/null || exit 1
1100                                         cat hat3 >> hat3.seed
1101 #                                       echo "$1"
1102                                         seedoffset=`expr $seedoffset + $1`
1103 #                                       echo "$1"
1104 #                                       echo "seedoffset="$seedoffset
1105                                 done;
1106 #                               echo "seedoffset="$seedoffset
1107                                 if [ $anysymbol -eq 1 ]; then
1108                                         "$prefix/replaceu" -i orig2 -o $seedoffset >> infile 2>/dev/null || exit 1  # yarinaoshi
1109                                         cat orig2 >> orig
1110                                 else
1111                                         cat infile2 >> infile
1112                                 fi
1113                         elif [ $seedtable != "x" ]; then
1114                                 cat _seedtablefile > hat3.seed
1115                         else
1116                                 cat /dev/null > hat3.seed
1117                         fi
1118 #                       cat hat3.seed
1119
1120
1121                         if [ $mccaskill -eq 1 ]; then
1122                                 "$prefix/mccaskillwrap" -C $numthreads -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
1123                         elif [ $contrafold -eq 1 ]; then
1124                                 "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>/dev/null || exit 1
1125                         fi
1126                         if [ $distance = "fasta" ]; then
1127                                 "$prefix/dndfast7" $swopt < infile > /dev/null  2>&1      || exit 1
1128                                 cat hat3.seed hat3 > hatx
1129                                 mv hatx hat3
1130                                 "$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
1131                         elif [ $distance = "blast" ]; then
1132                                 "$prefix/dndblast" < infile > /dev/null  2>&1      || exit 1
1133                                 cat hat3.seed hat3 > hatx
1134                                 mv hatx hat3
1135                                 "$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
1136                         elif [ $distance = "foldalignlocal" ]; then
1137                                 "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null  2>&1      || exit 1
1138                                 cat hat3.seed hat3 > hatx
1139                                 mv hatx hat3
1140                                 "$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
1141                         elif [ $distance = "foldalignglobal" ]; then
1142                                 "$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
1143                                 cat hat3.seed hat3 > hatx
1144                                 mv hatx hat3
1145                                 "$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
1146                         elif [ $distance = "slara" ]; then
1147                                 "$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null  2>&1      || exit 1
1148                                 cat hat3.seed hat3 > hatx
1149                                 mv hatx hat3
1150                                 "$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
1151                         elif [ $distance = "lara" ]; then
1152                                 "$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null  2>&1      || exit 1
1153                                 cat hat3.seed hat3 > hatx
1154                                 mv hatx hat3
1155                                 "$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
1156                         elif [ $distance = "scarna" ]; then
1157                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null  2>&1      || exit 1
1158                                 cat hat3.seed hat3 > hatx
1159                                 mv hatx hat3
1160                                 "$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
1161                         elif [ $distance = "global" ]; then
1162                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -F < infile > /dev/null  2>&1      || exit 1
1163                                 cat hat3.seed hat3 > hatx
1164                                 mv hatx hat3
1165                                 "$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
1166                         elif [ $distance = "local" ]; then
1167                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $lexp -f $lgop  -h $laof -L < infile > /dev/null  2>&1      || exit 1
1168                                 cat hat3.seed hat3 > hatx
1169                                 mv hatx hat3
1170                                 "$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
1171                         elif [ $distance = "globalgenaf" ]; then
1172                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null 2>&1    || exit 1
1173                                 cat hat3.seed hat3 > hatx
1174                                 mv hatx hat3
1175                                 "$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
1176                         elif [ $distance = "localgenaf" ]; then
1177                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N < infile > /dev/null  2>&1      || exit 1
1178                                 cat hat3.seed hat3 > hatx
1179                                 mv hatx hat3
1180                                 "$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
1181                         elif [ $distance = "distonly" ]; then
1182                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null  2>&1      || exit 1
1183                                 "$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
1184                         elif [ $distance = "parttree" ]; then
1185                                 "$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre 2>/dev/null || exit 1
1186                                 mv hat3.seed hat3
1187                         else
1188                                 "$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
1189                                 mv hat3.seed hat3
1190                         fi
1191                         while [ $cycle -gt 1 ]
1192                         do
1193                                 if [ $distance = "parttree" ]; then
1194                                         mv pre infile
1195                                         "$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre 2>/dev/null || exit 1
1196                                 else
1197                                         "$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
1198                                 fi
1199                                 cycle=`expr $cycle - 1`
1200                         done
1201                         if [ $iterate -gt 0 ]; then
1202                                 if [ $distance = "sixtuples" ]; then
1203                                     "$prefix/dndpre" -C $numthreads < pre     > /dev/null 2>&1 || exit 1
1204                                 fi
1205                                 "$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
1206                         fi
1207                 else
1208
1209                         if [ $anysymbol -eq 1 ]; then
1210                                 mv infile orig
1211                                 "$prefix/replaceu" -i orig > infile || exit 1
1212                         fi
1213
1214                         if [ $seed != "x" ]; then
1215                                 mv infile infile2
1216                                 if [ $anysymbol -eq 1 ]; then
1217                                         mv orig orig2
1218                                         cat /dev/null > orig
1219                                 fi
1220                                 cat /dev/null > infile
1221                                 cat /dev/null > hat3.seed
1222                                 seedoffset=0
1223 #                               echo "seednseq="$seednseq
1224 #                               echo "seedoffset="$seedoffset
1225                                 set $seednseq > /dev/null
1226 #                               echo $#
1227                                 while [ $# -gt 1 ]
1228                                 do
1229                                         shift
1230 #                                       echo "num="$#
1231
1232                                         if [ $anysymbol -eq 1 ]; then
1233                                                 cat seed$# >> orig
1234                                                 "$prefix/replaceu" -i seed$# -o $seedoffset > clean || exit 1
1235                                                 mv clean seed$#
1236                                         fi
1237                                         "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile || exit 1
1238                                         cat hat3 >> hat3.seed
1239 #                                       echo "$1"
1240                                         seedoffset=`expr $seedoffset + $1`
1241 #                                       echo "$1"
1242 #                                       echo "seedoffset="$seedoffset
1243                                 done;
1244 #                               echo "seedoffset="$seedoffset
1245                                 if [ $anysymbol -eq 1 ]; then
1246                                         "$prefix/replaceu" -i orig2 -o $seedoffset >> infile || exit 1 # yarinaoshi
1247                                         cat orig2 >> orig
1248                                 else
1249                                         cat infile2 >> infile
1250                                 fi
1251                         elif [ $seedtable != "x" ]; then
1252                                 cat _seedtablefile > hat3.seed
1253                         else
1254                                 cat /dev/null > hat3.seed
1255                         fi
1256 #                       cat hat3.seed
1257
1258                         if [ $mccaskill -eq 1 ]; then
1259                                 "$prefix/mccaskillwrap" -C $numthreads -d "$prefix" -i infile > hat4  || exit 1
1260                         elif [ $contrafold -eq 1 ]; then
1261                                 "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4  || exit 1
1262                         fi
1263                         if [ $distance = "fasta" ]; then
1264                                 "$prefix/dndfast7" $swopt < infile > /dev/null     || exit 1
1265                                 cat hat3.seed hat3 > hatx
1266                                 mv hatx hat3
1267                                 "$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
1268                         elif [ $distance = "blast" ]; then
1269                                 "$prefix/dndblast" < infile > /dev/null     || exit 1
1270                                 cat hat3.seed hat3 > hatx
1271                                 mv hatx hat3
1272                                 "$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
1273                         elif [ $distance = "foldalignlocal" ]; then
1274                                 "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -h $laof -H -d "$prefix" < infile > /dev/null || exit 1
1275                                 cat hat3.seed hat3 > hatx
1276                                 mv hatx hat3
1277                                 "$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
1278                         elif [ $distance = "foldalignglobal" ]; then
1279                                 "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop  -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null || exit 1
1280                                 cat hat3.seed hat3 > hatx
1281                                 mv hatx hat3
1282                                 "$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
1283                         elif [ $distance = "slara" ]; then
1284                                 "$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop  -T -d "$prefix" < infile > /dev/null || exit 1
1285                                 cat hat3.seed hat3 > hatx
1286                                 mv hatx hat3
1287                                 "$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
1288                         elif [ $distance = "lara" ]; then
1289                                 "$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop  -B -d "$prefix" < infile > /dev/null || exit 1
1290                                 cat hat3.seed hat3 > hatx
1291                                 mv hatx hat3
1292                                 "$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
1293                         elif [ $distance = "scarna" ]; then
1294                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -f $pggop  -s -d "$prefix" < infile > /dev/null   || exit 1
1295                                 cat hat3.seed hat3 > hatx
1296                                 mv hatx hat3
1297                                 "$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
1298                         elif [ $distance = "global" ]; then
1299                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof   -F  < infile > /dev/null     || exit 1
1300                                 cat hat3.seed hat3 > hatx
1301                                 mv hatx hat3
1302                                 "$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
1303                         elif [ $distance = "local" ]; then
1304                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $lexp -f $lgop  -h $laof -L  < infile > /dev/null     || exit 1
1305                                 cat hat3.seed hat3 > hatx
1306                                 mv hatx hat3
1307                                 "$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
1308                         elif [ $distance = "globalgenaf" ]; then
1309                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $pgexp -f $pggop  -h $pgaof -O $GGOP -E $GEXP -K  < infile > /dev/null     || exit 1
1310                                 cat hat3.seed hat3 > hatx
1311                                 mv hatx hat3
1312                                 "$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
1313                         elif [ $distance = "localgenaf" ]; then
1314                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -g $lexp -f $lgop  -h $laof -O $LGOP -E $LEXP -N  < infile > /dev/null     || exit 1
1315                                 cat hat3.seed hat3 > hatx
1316                                 mv hatx hat3
1317                                 "$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
1318                         elif [ $distance = "distonly" ]; then
1319                                 "$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop  -h $pgaof  -t < infile > /dev/null            || exit 1
1320                                 "$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
1321                         elif [ $distance = "parttree" ]; then
1322                                 "$prefix/splittbfast" -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile   > pre || exit 1
1323                                 mv hat3.seed hat3
1324                         else
1325                                 "$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
1326                                 mv hat3.seed hat3
1327                         fi
1328
1329                         while [ $cycle -gt 1 ]
1330                         do
1331                                 if [ $distance = "parttree" ]; then
1332                                         mv pre infile
1333                                         "$prefix/splittbfast" -Z -Q $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop  -h "-"$aof  $param_fft -p $partsize -s $groupsize $treealg -i infile  > pre || exit 1
1334                                 else
1335                                         "$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
1336                                 fi
1337                                 cycle=`expr $cycle - 1`
1338                         done
1339                         if [ $iterate -gt 0 ]; then
1340                                 if [ $distance = "sixtuples" ]; then
1341                                 "$prefix/dndpre" -C $numthreads < pre     > /dev/null 2>&1 || exit 1
1342                                 fi
1343                                 "$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
1344                         fi
1345                 fi
1346
1347                 if [ $coreout -eq 1 ]; then
1348                         "$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2
1349                         mv pre2 pre
1350                 elif [ $anysymbol -eq 1 ]; then
1351                         "$prefix/restoreu" -a pre -i orig > restored || exit 1
1352                         mv restored pre
1353                 fi
1354
1355                 if [ $quiet -eq 0 ]; then
1356                         echo '' 1>&2
1357                         if [ $mccaskill -eq 1 ]; then
1358                                 echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>&2
1359                                 echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>&2
1360                                 echo "incorporated in the iterative alignment process (4)." 1>&2
1361                                 echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>&2
1362                                 echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>&2
1363                                 echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>&2
1364                                 echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
1365                                 echo "" 1>&2
1366                         elif [ $contrafold -eq 1 ]; then
1367                                 echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>&2
1368                                 echo "and then incorporated in the iterative alignment process (4)." 1>&2
1369                                 echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>&2
1370                                 echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>&2
1371                                 echo "" 1>&2
1372                         fi
1373                         if [ $distance = "fasta" -o $partdist = "fasta" ]; then
1374                                 echo "Pairwise alignments were computed by FASTA" 1>&2
1375                                 echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>&2
1376                         fi
1377                         if [ $distance = "blast" ]; then
1378                                 echo "Pairwise alignments were computed by BLAST" 1>&2
1379                                 echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>&2
1380                         fi
1381                         if [ $distance = "scarna" ]; then
1382                                 echo "Pairwise alignments were computed by MXSCARNA" 1>&2
1383                                 echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>&2
1384                         fi
1385                         if [ $distance = "lara" -o $distance = "slara" ]; then
1386                                 echo "Pairwise alignments were computed by LaRA" 1>&2
1387                                 echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>&2
1388                         fi
1389                         if [ $distance = "foldalignlocal" ]; then
1390                                 echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>&2
1391                                 echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
1392                         fi
1393                         if [ $distance = "foldalignglobal" ]; then
1394                                 echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>&2
1395                                 echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>&2
1396                         fi
1397                         printf "\n" 1>&2
1398                         echo 'Strategy:' 1>&2
1399                         printf ' '$strategy 1>&2
1400                         echo ' ('$performance')' 1>&2
1401                         echo ' '$explanation 1>&2
1402                         echo '' 1>&2
1403                         echo "If unsure which option to use, try 'mafft --auto input > output'." 1>&2
1404 #                       echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>&2
1405                         echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>&2
1406                         echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>&2
1407                         echo '' 1>&2
1408                 fi
1409         )
1410
1411         if [ "$outputfile" = "" ]; then
1412                 if [ "$outputopt" = "null" ]; then
1413                         cat < $TMPFILE/pre || exit 1
1414                 else
1415                         "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre || exit 1
1416                 fi
1417         else
1418                 if [ "$outputopt" = "null" ]; then
1419                         cat < $TMPFILE/pre > "$outputfile" || exit 1
1420                 else
1421                         "$prefix/f2cl" -n $namelength $outputopt < $TMPFILE/pre > "$outputfile" || exit 1
1422                 fi
1423         fi
1424
1425         if [ $treeout -eq 1 ]; then
1426                 cp $TMPFILE/infile.tree "$infilename.tree"
1427         fi
1428
1429         if [ $distout -eq 1 ]; then
1430                 cp $TMPFILE/hat2 "$infilename.hat2"
1431         fi
1432
1433         exit 0;
1434 fi
1435
1436 prog="awk"
1437
1438 tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
1439 if [ -x "$tmpawk" ]; then
1440         prog="$tmpawk"
1441 fi
1442
1443 tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
1444 if [ -x "$tmpawk" ]; then
1445         prog="$tmpawk"
1446 fi
1447
1448 #echo "prog="$prog 1>&2
1449
1450 umask 077
1451 (
1452 $prog '
1453 BEGIN {
1454         prefix = ENVIRON["prefix"];
1455         version = ENVIRON["version"];
1456         myself = ENVIRON["myself"];
1457         while( 1 )
1458         {
1459                 options = ""
1460                 printf( "\n" ) > "/dev/tty";
1461                 printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
1462                 printf( "\n" )                                                                           > "/dev/tty";
1463                 printf( "   MAFFT %s\n", version )                                                       > "/dev/tty";
1464                 printf( "\n" )                                                                           > "/dev/tty";
1465                 printf( "        Copyright (c) 2011 Kazutaka Katoh\n" )                                  > "/dev/tty";
1466                 printf( "        NAR 30:3059-3066, NAR 33:511-518\n" )                                   > "/dev/tty";
1467                 printf( "        http://mafft.cbrc.jp/alignment/software/\n" )       > "/dev/tty";
1468                 printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
1469                 printf( "\n" ) > "/dev/tty";
1470
1471                 while( 1 )
1472                 {
1473                         printf( "\n" ) > "/dev/tty";
1474                         printf( "Input file? (fasta format)\n@ " ) > "/dev/tty";
1475                         res = getline < "/dev/tty";
1476                         close( "/dev/tty" )
1477                         if( res == 0 || NF == 0 )
1478                                 continue;
1479                         infile = sprintf( "%s", $0 );
1480
1481                         res = getline < infile;
1482                         close( infile );
1483                         if( res == -1 )
1484                         {
1485                                 printf( "%s: No such file.\n\n", infile ) > "/dev/tty";
1486                                 printf( "Filename extension (eg., .txt) must be typed, if any.\n\n" ) > "/dev/tty";
1487                         }
1488                         else if( res == 0 )
1489                                 printf( "%s: Empty.\n", infile ) > "/dev/tty";
1490                         else
1491                         {
1492                                 printf( "OK. infile = %s\n\n", infile ) > "/dev/tty";
1493                                 break;
1494                         }
1495                 }
1496                 nseq = 0;
1497
1498                 while( 1 )
1499                 {
1500                         printf( "\n" ) > "/dev/tty";
1501                         printf( "Output file?\n" ) > "/dev/tty";
1502                         printf( "@ " ) > "/dev/tty";
1503                         res = getline < "/dev/tty";
1504                         close( "/dev/tty" );
1505                         if( res == 0 || NF == 0 )
1506                                 continue;
1507                         else
1508                         {
1509                                 outfile = sprintf( "%s", $0 );
1510                                 printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
1511                                 break;
1512                         }
1513                 }
1514
1515                 while( 1 )
1516                 {
1517                         outargs = "";
1518                         printf( "\n" ) > "/dev/tty";
1519                         printf( "Output format?\n" ) > "/dev/tty";
1520                         printf( "  1. Clustal format / Sorted\n" ) > "/dev/tty";
1521                         printf( "  2. Clustal format / Input order\n" ) > "/dev/tty";
1522                         printf( "  3. Fasta format   / Sorted\n" ) > "/dev/tty";
1523                         printf( "  4. Fasta format   / Input order\n" ) > "/dev/tty";
1524                         printf( "  5. Phylip format  / Sorted\n" ) > "/dev/tty";
1525                         printf( "  6. Phylip format  / Input order\n" ) > "/dev/tty";
1526                         printf( "@ " ) > "/dev/tty";
1527                         res = getline < "/dev/tty";
1528                         close( "/dev/tty" );
1529 #                       printf( "res=%d, NF=%d\n", res, NF );
1530
1531                         resnum = 0 + $1;
1532 #                       printf( "resnum=%d\n", resnum );
1533
1534                         if( resnum < 1 || 6 < resnum )
1535                                 continue;
1536                         else
1537                         {
1538                                 if( resnum == 1 )
1539                                         outargs = "--clustalout --reorder";
1540                                 else if( resnum == 2 )
1541                                         outargs = "--clustalout --inputorder";
1542                                 else if( resnum == 3 )
1543                                         outargs = "--reorder";
1544                                 else if( resnum == 4 )
1545                                         outargs = "--inputorder";
1546                                 else if( resnum == 5 )
1547                                         outargs = "--phylipout --reorder";
1548                                 else if( resnum == 6 )
1549                                         outargs = "--phylipout --inputorder";
1550                                 else
1551                                         continue;
1552                                 printf( "OK. arguments = %s\n\n", outargs ) > "/dev/tty";
1553                                 break;
1554                         }
1555                 }
1556
1557                 while( 1 )
1558                 {
1559                         arguments = "";
1560                         printf( "\n" ) > "/dev/tty";
1561                         printf( "Strategy?\n" ) > "/dev/tty";
1562                         printf( "  1. --auto\n" ) > "/dev/tty";
1563                         printf( "  2. FFT-NS-1 (fast)\n" ) > "/dev/tty";
1564                         printf( "  3. FFT-NS-2 (default)\n" ) > "/dev/tty";
1565                         printf( "  4. G-INS-i  (accurate)\n" ) > "/dev/tty";
1566                         printf( "  5. L-INS-i  (accurate)\n" ) > "/dev/tty";
1567                         printf( "  6. E-INS-i  (accurate)\n" ) > "/dev/tty";
1568                         printf( "@ " ) > "/dev/tty";
1569                         res = getline < "/dev/tty";
1570                         close( "/dev/tty" );
1571 #                       printf( "res=%d, NF=%d\n", res, NF );
1572
1573                         resnum = 0 + $1;
1574 #                       printf( "resnum=%d\n", resnum );
1575
1576                         if( resnum < 1 || 6 < resnum )
1577                                 continue;
1578                         else
1579                         {
1580                                 if( resnum == 1 )
1581                                         arguments = "--auto";
1582                                 else if( resnum == 2 )
1583                                         arguments = "--retree 1";
1584                                 else if( resnum == 3 )
1585                                         arguments = "--retree 2";
1586                                 else if( resnum == 4 )
1587                                         arguments = "--globalpair --maxiterate 16";
1588                                 else if( resnum == 5 )
1589                                         arguments = "--localpair  --maxiterate 16";
1590                                 else if( resnum == 6 )
1591                                         arguments = "--genafpair  --maxiterate 16";
1592                                 else
1593                                         arguments = sprintf( "%s", $0 );
1594                                 printf( "OK. arguments = %s %s\n\n", arguments, outargs ) > "/dev/tty";
1595                                 break;
1596                         }
1597                 }
1598
1599
1600                 while( 1 )
1601                 {
1602                         printf( "\n" ) > "/dev/tty";
1603                         printf( "Additional arguments? (--ep #, --op #, --kappa #, etc)\n" ) > "/dev/tty";
1604                         printf( "@ " ) > "/dev/tty";
1605                         res = getline < "/dev/tty";
1606                         close( "/dev/tty" );
1607                         if( res == 0 || NF == 0 )
1608                         {
1609                                 break;
1610                         }
1611                         else
1612                         {
1613                                 addargs = sprintf( "%s", $0 );
1614                                 printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty";
1615                                 break;
1616                         }
1617                 }
1618
1619                 arguments = sprintf( "%s %s %s", addargs, arguments, outargs );
1620
1621                 print ""
1622                 command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile );
1623                 gsub( /\\/, "/", command );
1624
1625
1626                 printf( "command=\n%s\n", command ) > "/dev/tty";
1627
1628
1629                 while( 1 )
1630                 {
1631                         go = 0;
1632                         printf( "OK?\n" ) > "/dev/tty";
1633                         printf( "@ [Y] " ) > "/dev/tty";
1634                         res = getline < "/dev/tty";
1635                         close( "/dev/tty" );
1636                         if( res == 0 )
1637                                 continue;
1638                         else if( NF == 0 || $0 ~ /^[Yy]/ )
1639                         {
1640                                 go=1;
1641                                 break;
1642                         }
1643                         else
1644                                 break;
1645                 }
1646                 if( go ) break;
1647                 printf( "\n" ) > "/dev/tty";
1648                 printf( "\n" ) > "/dev/tty";
1649         }
1650         system( command );
1651         command = sprintf( "less \"%s\"", outfile );
1652         system( command );
1653         printf( "Press Enter to exit." ) > "/dev/tty";
1654         res = getline < "/dev/tty";
1655 }
1656 '
1657 )
1658 exit 0;