/var/lib/mobyle/programs/dnapars.xml is in mobyle-programs 5.1.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 | <?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>dnapars</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
<doc>
<title>dnapars</title>
<description>
<text lang="en">DNA Parsimony Program</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/dnapars.html</doclink>
<comment>
<text lang="en">This program carries out unrooted parsimony (analogous to Wagner trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA sequences. The method of Fitch (1971) is used to count the number of changes of base needed on a given tree.</text>
</comment>
</doc>
<category>phylogeny:parsimony</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>dnapars</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"dnapars <dnapars.params"</code>
<code proglang="python">"dnapars <dnapars.params"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>infile</name>
<prompt lang="en">Alignment File (infile)</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>PHYLIPI</dataFormat>
</type>
<precond>
<code proglang="perl">$infile ne "infile"</code>
<code proglang="python">infile != "infile"</code>
</precond>
<format>
<code proglang="perl">"ln -s $infile infile && "</code>
<code proglang="python">"ln -s " + str( infile ) + " infile && "</code>
</format>
<ctrl>
<message>
<text lang="en">the name of this data can't be "infile","outfile","outtree","intree"</text>
</message>
<code proglang="python">value not in ( "outfile" , "infile" , "outtree" , "intree")</code>
<code proglang="perl">$value ne "outfile" and $value ne "infile" and $value ne "outtree" and $value ne "intree"</code>
</ctrl>
<argpos>-10</argpos>
<comment>
<text lang="en">The input file must contained aligned sequences in PHYLIP format obtained by sequence alignment programs.</text>
</comment>
<example>
5 13
Alpha AACGTGGCCACAT
Beta AAGGTCGCCACAC
Gamma CAGTTCGCCACAA
Delta GAGATTTCCGCCT
Epsilon GAGATCTCCGCCC
</example>
</parameter>
<paragraph>
<name>dnapars_opt</name>
<prompt lang="en">Parsimony options</prompt>
<parameters>
<parameter>
<name>use_threshold</name>
<prompt lang="en">Use Threshold parsimony (T)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "T\\n$threshold\\n" : ""</code>
<code proglang="python">( "" , "T\n" + str( threshold ) + "\n" )[ value ]</code>
</format>
<argpos>2</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>threshold</name>
<prompt lang="en">Value for threshold parsimony</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$use_threshold</code>
<code proglang="python">use_threshold</code>
</precond>
<ctrl>
<message>
<text lang="en">You must enter a numeric value, greater than 1</text>
</message>
<code proglang="perl">$threshold > 1</code>
<code proglang="python">threshold > 1</code>
</ctrl>
<argpos>3</argpos>
<comment>
<text lang="en">Thresholds less than or equal to 1.0 do not have any meaning and should not be used: they will result in a tree dependent only on the input order of species and not at all on the data</text>
</comment>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter>
<name>use_transversion</name>
<prompt lang="en">Use Transversion parsimony (N)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "N\\n" : ""</code>
<code proglang="python">( "" , "N\n" )[ value ]</code>
</format>
<argpos>5</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>bootstrap</name>
<prompt lang="en">Bootstrap options ( multiple dataset )</prompt>
<parameters>
<parameter issimple="1">
<name>seqboot</name>
<prompt lang="en">Perform a bootstrap before analysis</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "seqboot <seqboot.params && mv outfile seqboot.outfile && rm infile && ln -s seqboot.outfile infile && " : ""</code>
<code proglang="python">( "" , "seqboot <seqboot.params && mv outfile seqboot.outfile && rm infile && ln -s seqboot.outfile infile && " )[ value ]</code>
</format>
<ctrl>
<message>
<text lang="en">you can't use "Randomize options" and "Bootstrap options" at the same time</text>
</message>
<code proglang="perl">not( $seqboot and $jumble)</code>
<code proglang="python">not( seqboot and jumble)</code>
</ctrl>
<argpos>-5</argpos>
<comment>
<text lang="en">By selecting this option, the bootstrap will be performed on your sequence file. So you don't need to perform a separated seqboot before.</text>
<text lang="en">Don't give an already bootstrapped file to the program, this won't work!</text>
<text lang="en">You can't use "Randomize options" and "Bootstrap options" at the same time.</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>Method</name>
<prompt lang="en">Resampling methods (J)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<vdef>
<value>bootstrap</value>
</vdef>
<flist>
<felem>
<value>bootstrap</value>
<label>Bootstrap</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>jackknife</value>
<label>Delete-half jackknife</label>
<code proglang="perl">"J\\n"</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>permute_species</value>
<label>Permute species for each character</label>
<code proglang="perl">"J\\nJ\\n"</code>
<code proglang="python">"J\nJ\n"</code>
</felem>
<felem>
<value>permute_char</value>
<label>Permute character order</label>
<code proglang="perl">"J\\nJ\\nJ\\n"</code>
<code proglang="python">"J\nJ\nJ\n"</code>
</felem>
<felem>
<value>permute_within_species</value>
<label>Permute within species</label>
<code proglang="perl">"J\\nJ\\nJ\\nJ\\n"</code>
<code proglang="python">"J\nJ\nJ\nJ\n"</code>
</felem>
</flist>
<argpos>1</argpos>
<comment>
<text lang="en">
1. The bootstrap. Bootstrapping was invented by Bradley Efron in 1979, and its use in phylogeny estimation was introduced by me (Felsenstein, 1985b). It involves creating a new data set by sampling N characters randomly with replacement, so that the resulting data set has the same size as the original, but some characters have been left out and others are duplicated. The random variation of the results from analyzing these bootstrapped data sets can be shown statistically to be
typical of the variation that you would get from collecting new data sets. The method assumes that the characters evolve independently, an assumption that may not be realistic for many kinds of data.
</text>
<text lang="en">
2. Delete-half-jackknifing. This alternative to the bootstrap involves sampling a random half of the characters, and including them in the data but dropping the others. The resulting data sets are half the size of the original, and no characters are duplicated. The random variation from doing this should be very similar to that obtained from the bootstrap. The method is advocated by Wu (1986).
</text>
<text lang="en">
3. Permuting species for each characters. This method of resampling (well, OK, it may not be best to call it resampling) was introduced by Archie (1989) and Faith (1990; see also Faith and Cranston, 1991). It involves permuting the columns of the data matrix separately. This produces data matrices that have the same number and kinds of characters but no taxonomic structure. It is used for different purposes than the bootstrap, as it tests not the variation around an estimated tree but the hypothesis that there is no taxonomic structure in the data: if a statistic such as number of steps is significantly smaller in the actual data than it is in replicates that are permuted, then we can argue that there is some taxonomic structure in the data (though perhaps it might be just the presence of aa pair of sibling species).
</text>
<text lang="en">
4. Permuting characters order. This simply permutes the order of the characters, the same reordering being applied to all species. For many methods of tree inference this will make no difference to the outcome (unless one has rates of evolution correlated among adjacent sites). It is included as a possible step in carrying out a permutation test of homogeneity of characters (such as the Incongruence Length Difference test).
</text>
<text lang="en">
5. Permuting characters separately for each species. This is a method introduced by Steel, Lockhart, and Penny (1993) to permute data so as to destroy all phylogenetic structure, while keeping the base composition of each species the same as before. It shuffles the character order separately for each species.
</text>
</comment>
<paramfile>seqboot.params</paramfile>
</parameter>
<parameter issimple="1">
<name>replicates</name>
<prompt lang="en">How many replicates (R)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<vdef>
<value>100</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "R\\n$value\\n" : ""</code>
<code proglang="python">( "" , "R\n" + str( value ) +"\n" )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">This server allows no more than 1000 replicates</text>
</message>
<code proglang="perl">$replicates <= 1000</code>
<code proglang="python">replicates <= 1000</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Bad data sets number: it must be greater than 1</text>
</message>
<code proglang="perl">$value > 1</code>
<code proglang="python">value > 1</code>
</ctrl>
<argpos>1</argpos>
<paramfile>seqboot.params</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>seqboot_seed</name>
<prompt lang="en">Random number seed (must be odd)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<format>
<code proglang="perl">"$value\\n"</code>
<code proglang="python">str( value ) + "\n"</code>
</format>
<ctrl>
<message>
<text lang="en">Random number seed must be odd</text>
</message>
<code proglang="perl">$value > 0 and (($value % 2) != 0)</code>
<code proglang="python">value > 0 and (( value % 2 ) != 0 )</code>
</ctrl>
<argpos>1010</argpos>
<paramfile>seqboot.params</paramfile>
</parameter>
<parameter issimple="1">
<name>seqboot_times2jumble</name>
<prompt lang="en">Number of times to jumble</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<ctrl>
<message>
<text lang="en">the product of "number of times to jumble" and replicates must be less than 100000</text>
</message>
<code proglang="perl">($seqboot_times2jumble * (defined $replicates) ? $replicates : 1) <= 100000</code>
<code proglang="python">seqboot_times2jumble * ( 1 , replicates)[replicates is not None] <= 100000</code>
</ctrl>
</parameter>
<parameter ishidden="1">
<name>multiple_dataset</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<format>
<code proglang="perl">"M\\nD\\n$replicates\\n$seqboot_seed\\n$times2jumble\\n"</code>
<code proglang="python">"M\nD\n" + str( replicates ) + "\n" + str(seqboot_seed) + "\n"+ str( seqboot_times2jumble ) + "\n"</code>
</format>
<argpos>1</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>bootconfirm</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<format>
<code proglang="perl">"Y\\n"</code>
<code proglang="python">"Y\n"</code>
</format>
<argpos>1000</argpos>
<paramfile>seqboot.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>bootterminal_type</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<format>
<code proglang="perl">"0\\n"</code>
<code proglang="python">"0\n"</code>
</format>
<argpos>-1</argpos>
<paramfile>seqboot.params</paramfile>
</parameter>
<parameter issimple="1">
<name>consense</name>
<prompt lang="en">Compute a consensus tree</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot and $print_treefile</code>
<code proglang="python">seqboot and print_treefile</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " && cp infile dnapars.infile && cp dnapars.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" : ""</code>
<code proglang="python">( "" , " && cp infile dnapars.infile && cp dnapars.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" )[ value ]</code>
</format>
<argpos>100</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>jumble_opt</name>
<prompt lang="en">Randomize options ( one dataset )</prompt>
<comment>
<text lang="en">Use these options only if you have only one data set</text>
</comment>
<parameters>
<parameter>
<name>jumble</name>
<prompt lang="en">Randomize (jumble) input order (J)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value and not $seqboot )? "J\\n$jumble_seed\\n$jumble_times\\n" : ""</code>
<code proglang="python">( "" , "J\n" + str( jumble_seed ) + "\n" + str( jumble_times ) +"\n" )[ value and not seqboot ]</code>
</format>
<ctrl>
<message>
<text lang="en">you can't use "Randomize options" and "Bootstrap options" at the same times</text>
</message>
<code proglang="perl">not( $jumble and $seqboot)</code>
<code proglang="python">not (jumble and seqboot)</code>
</ctrl>
<argpos>20</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>jumble_seed</name>
<prompt lang="en">Random number seed for jumble (must be odd)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$jumble</code>
<code proglang="python">jumble</code>
</precond>
<ctrl>
<message>
<text lang="en">Random number seed for jumble must be odd.</text>
</message>
<code proglang="perl">defined $value and ($value > 0 and (($value % 2) != 0))</code>
<code proglang="python">value is not None and (value > 0 and ((value % 2) != 0))</code>
</ctrl>
</parameter>
<parameter ismandatory="1">
<name>jumble_times</name>
<prompt lang="en">Number of times to jumble</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$jumble</code>
<code proglang="python">jumble</code>
</precond>
<vdef>
<value>1</value>
</vdef>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>user_tree_opt</name>
<prompt lang="en">User tree options</prompt>
<parameters>
<parameter>
<name>user_tree</name>
<prompt lang="en">Use User tree (default: no, search for best tree) (U)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "U\\n" : ""</code>
<code proglang="python">( "" , "U\n" )[ value ]</code>
</format>
<ctrl>
<message>
<text lang="en">You cannot bootstrap your dataset and give a user tree at the same time</text>
</message>
<code proglang="perl">not ( $user_tree and $seqboot )</code>
<code proglang="python">not ( user_tree and seqboot )</code>
</ctrl>
<ctrl>
<message>
<text lang="en">you cannot randomize (jumble) your dataset and give a user tree at the same time</text>
</message>
<code proglang="perl">not ( $user_tree and $jumble )</code>
<code proglang="python">not ( user_tree and jumble )</code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">To give your tree to the program, you must normally put it in the alignment file, after the sequences, preceded by a line indicating how many trees you give.</text>
<text lang="en">Here, this will be automatically appended: just give a treefile and the number of trees in it.</text>
</comment>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>tree_file</name>
<prompt lang="en">User Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$user_tree</code>
<code proglang="python">user_tree</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? "ln -s $tree_file intree; " : ""</code>
<code proglang="python">( "" , "ln -s " + str( tree_file ) + " intree; " )[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">the name of this data can't be "infile","outfile","outtree","intree"</text>
</message>
<code proglang="python">value not in ( "outfile" , "infile" , "outtree" ,"intree" )</code>
<code proglang="perl">$value ne "outfile" and $value ne "infile" and $value ne "outtree" and $value ne "intree"</code>
</ctrl>
<argpos>-1</argpos>
<comment>
<text lang="en">Give a tree whenever the infile does not already contain the tree.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>weight_opt</name>
<prompt lang="en">Weight options</prompt>
<parameters>
<parameter>
<name>weights</name>
<prompt lang="en">Use weights for sites (W)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "W\\n" : ""</code>
<code proglang="python">( "" , "W\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>weights_file</name>
<prompt lang="en">Weights file</prompt>
<type>
<datatype>
<class>PhylipWeight</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$weights</code>
<code proglang="python">weights</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? "ln -s $weights_file weights; " : ""</code>
<code proglang="python">( "" , "ln -s " + str( weights_file ) + " weights; " )[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">the name of this data can't be "infile","outfile","outtree","intree"</text>
</message>
<code proglang="python">value not in ( "outfile" , "infile" , "outtree" ,"intree" )</code>
<code proglang="perl">$value ne "outfile" and $value ne "infile" and $value ne "outtree" and $value ne "intree"</code>
</ctrl>
<argpos>-1</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>print_tree</name>
<prompt lang="en">Print out tree (3)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : "3\\n"</code>
<code proglang="python">( "3\n" , "")[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Tells the program to print a semi-graphical picture of the tree in the outfile.</text>
</comment>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter>
<name>print_steps</name>
<prompt lang="en">Print out steps in each site (4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "4\\n" : ""</code>
<code proglang="python">( "" , "4\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter>
<name>print_sequences</name>
<prompt lang="en">Print sequences at all nodes of tree (5)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "5\\n" : ""</code>
<code proglang="python">( "" , "5\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter>
<name>print_treefile</name>
<prompt lang="en">Write out trees onto tree file (6)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : "6\\n"</code>
<code proglang="python">( "6\n" , "" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Tells the program to save the tree in a tree file (outtree) (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas).</text>
</comment>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter>
<name>printdata</name>
<prompt lang="en">Print out the data at start of run (1)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "1\\n" : ""</code>
<code proglang="python">( "" , "1\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>other_options</name>
<prompt lang="en">Other options</prompt>
<parameters>
<parameter>
<name>outgroup</name>
<prompt lang="en">Outgroup species (J)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "O\\n$value\\n" : ""</code>
<code proglang="python">( "" , "O\n" + str( value ) + "\n" )[ value is not None and value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">Please enter a value greater than 0</text>
</message>
<code proglang="perl">defined $value and $value > 0</code>
<code proglang="python">value is not None and value > 0</code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">The O (Outgroup) option specifies which species is to have the root of the tree be on the line leading to it.</text>
<text lang="en">For example, if the outgroup is a species "Mouse" then the root of the tree will be placed in the middle of the branch which is connected to this species, with Mouse branching off on one side of the root and the lineage leading to the rest of the tree on the other.</text>
<text lang="en">This option is toggle on by choosing the number of the outgroup (the species being taken in the numerical order that they occur in the input file).</text>
<text lang="en">Outgroup-rooting will not be attempted if it is a user-defined tree, despite your invoking the option.</text>
<text lang="en">When it is used, the tree as printed out is still listed as being an unrooted tree, though the outgroup is connected to the bottommost node so that it is easy to visually convert the tree into rooted form.</text>
</comment>
<paramfile>dnapars.params</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt lang="en">Outfile</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" && mv outfile dnapars.outfile"</code>
<code proglang="python">" && mv outfile dnapars.outfile"</code>
</format>
<argpos>40</argpos>
<filenames>
<code proglang="perl">dnapars.outfile</code>
<code proglang="python">'dnapars.outfile'</code>
</filenames>
</parameter>
<parameter isout="1">
<name>treefile</name>
<prompt lang="en">Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$print_treefile</code>
<code proglang="python">print_treefile</code>
</precond>
<format>
<code proglang="perl">" && mv outtree dnapars.outtree" </code>
<code proglang="python">" && mv outtree dnapars.outtree"</code>
</format>
<argpos>50</argpos>
<filenames>
<code proglang="perl">dnapars.outtree</code>
<code proglang="python">'dnapars.outtree'</code>
</filenames>
</parameter>
<parameter isout="1">
<name>seqboot_out</name>
<prompt lang="en">seqboot outfile</prompt>
<type>
<datatype>
<class>SetOfAlignment</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<argpos>40</argpos>
<filenames>
<code proglang="perl">"seqboot.outfile"</code>
<code proglang="python">"seqboot.outfile"</code>
</filenames>
</parameter>
<parameter ishidden="1">
<name>confirm</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"Y\\n"</code>
<code proglang="python">"Y\n"</code>
</format>
<argpos>1000</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>terminal_type</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"0\\n"</code>
<code proglang="python">"0\n"</code>
</format>
<argpos>-1</argpos>
<paramfile>dnapars.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>consense_confirm</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<format>
<code proglang="perl">"Y\\n"</code>
<code proglang="python">"Y\n"</code>
</format>
<argpos>1000</argpos>
<paramfile>consense.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>consense_terminal_type</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<format>
<code proglang="perl">"T\\n"</code>
<code proglang="python">"T\n"</code>
</format>
<argpos>-2</argpos>
<paramfile>consense.params</paramfile>
</parameter>
<parameter isout="1">
<name>consense_outfile</name>
<prompt lang="en">Consense outfile</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outfile"</code>
<code proglang="python">"consense.outfile"</code>
</filenames>
</parameter>
<parameter ishidden="1">
<name>consense_outgroup</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense and $outgroup and $outgroup > 1</code>
<code proglang="python">consense and outgroup and outgroup > 1</code>
</precond>
<format>
<code proglang="perl">"O\\n$outgroup\\n"</code>
<code proglang="python">"O\n" + str( outgroup ) + "\n"</code>
</format>
<argpos>1000</argpos>
<paramfile>consense.params</paramfile>
</parameter>
<parameter isout="1">
<name>consense_treefile</name>
<prompt lang="en">Consense tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outtree"</code>
<code proglang="python">"consense.outtree"</code>
</filenames>
</parameter>
</parameters>
</program>
|