/var/lib/mobyle/programs/fitch.xml is in mobyle-programs 5.1.2-1.
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 | <?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>fitch</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
<doc>
<title>fitch</title>
<description>
<text lang="en">Fitch-Margoliash and Least-Squares Distance Methods</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/fitch.html</doclink>
<comment>
<text lang="en">This program carries out Fitch-Margoliash,
Least Squares, and a number of similar methods</text>
</comment>
</doc>
<category>phylogeny:distance</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>fitch</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"fitch <fitch.params"</code>
<code proglang="python">"fitch <fitch.params"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>infile</name>
<prompt lang="en">Distances matrix File</prompt>
<type>
<datatype>
<class>PhylipDistanceMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$infile ne "infile"</code>
<code proglang="python">infile != "infile"</code>
</precond>
<format>
<code proglang="perl">"ln -s $infile infile && "</code>
<code proglang="python">"ln -s " + str( value ) + " infile && "</code>
</format>
<argpos>-5</argpos>
<comment>
<text lang="en">Give a file containing a distance matrix
obtained by distance matrix programs like protdist or
dnadist</text>
</comment>
<example>
5
Alpha 0.000000 0.330447 0.625670 1.032032 1.354086
Beta 0.330447 0.000000 0.375578 1.096290 0.677616
Gamma 0.625670 0.375578 0.000000 0.975798 0.861634
Delta 1.032032 1.096290 0.975798 0.000000 0.226703
Epsilon 1.354086 0.677616 0.861634 0.226703 0.000000
</example>
</parameter>
<parameter>
<name>Method</name>
<prompt lang="en">Method (D)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>FM</value>
</vdef>
<flist>
<felem>
<value>FM</value>
<label>Fitch-Margoliash</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>ME</value>
<label>Minimum Evolution</label>
<code proglang="perl">"D\\n"</code>
<code proglang="python">"D\n"</code>
</felem>
</flist>
<paramfile>fitch.params</paramfile>
</parameter>
<paragraph>
<name>fitch_options</name>
<prompt lang="en">Fitch options</prompt>
<parameters>
<parameter>
<name>negative_branch</name>
<prompt lang="en">Negative branch lengths allowed (-)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "-\\n" : ""</code>
<code proglang="python">( "" , "-\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>power</name>
<prompt lang="en">Power (P)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>2.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? "P\\n$value\\n" : ""</code>
<code proglang="python">( "" , "P\n" + str(value ) + "\n" )[ value is not None and value != vdef ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">For the Fitch-Margoliash method, which is the default method with this program, P is 2.0. For the Cavalli-Sforza and Edwards least squares method it should be set to 0 (so that the denominator is always 1). An intermediate method is also available in which P is 1.0, and any other value of P, such as 4.0 or -2.3, can also be used. This generates a whole family of methods.</text>
<text lang="en">Please read the documentation (man distance).</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>jumble_options</name>
<prompt lang="en">Randomize options</prompt>
<parameters>
<parameter>
<name>jumble</name>
<prompt lang="en">Randomize (jumble) input order (J)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $user_tree</code>
<code proglang="python">not user_tree</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "J\\n$jumble_seed\\n$jumble_number\\n" : ""</code>
<code proglang="python">( "" , "J\n"+str( jumble_seed ) +"\n" + str( jumble_number ) +"\n" )[ value ]</code>
</format>
<argpos>20</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>jumble_seed</name>
<prompt lang="en">Random number seed (must be odd)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$jumble</code>
<code proglang="python">jumble</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">Random number seed must be odd</text>
</message>
<code proglang="perl">$value > 0 and ($value % 2) != 0</code>
<code proglang="python">value > 0 and (value % 2) != 0</code>
</ctrl>
<argpos>19</argpos>
</parameter>
<parameter>
<name>jumble_number</name>
<prompt lang="en">Number of times to jumble</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$jumble</code>
<code proglang="python">jumble</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<argpos>19</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>bootstrap</name>
<prompt lang="en">Bootstrap options</prompt>
<parameters>
<parameter>
<name>multiple</name>
<prompt lang="en">Analyze multiple data sets (M)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "M\\n$multiple_number\\n$multiple_seed\\n" : ""</code>
<code proglang="python">( "", "M\n"+str(multiple_number)+"\n"+str(multiple_seed)+"\n")[value]</code>
</format>
<argpos>10</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>multiple_number</name>
<prompt lang="en">How many data sets</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$multiple</code>
<code proglang="python">multiple</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">There must be no more than 1000 datasets for this server</text>
</message>
<code proglang="perl">$value <= 1000</code>
<code proglang="python">value <= 1000</code>
</ctrl>
<argpos>9</argpos>
</parameter>
<parameter ismandatory="1">
<name>multiple_seed</name>
<prompt lang="en">Random number seed (must be odd)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$multiple</code>
<code proglang="python">multiple</code>
</precond>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</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>19</argpos>
</parameter>
<parameter>
<name>consense</name>
<prompt lang="en">Compute a consensus tree</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$multiple and $print_treefile</code>
<code proglang="python">multiple and print_treefile</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " && cp infile fitch.infile && cp fitch.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" : ""</code>
<code proglang="python">( "" , " && cp infile fitch.infile && cp fitch.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" )[ value ]</code>
</format>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<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>Consense output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outfile"</code>
<code proglang="python">"consense.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>consense_treefile</name>
<prompt>Consense tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$consense</code>
<code proglang="python">consense</code>
</precond>
<filenames>
<code proglang="perl">"consense.outtree"</code>
<code proglang="python">"consense.outtree"</code>
</filenames>
</parameter>
<paragraph>
<name>user_tree_opt</name>
<prompt lang="en">User tree options</prompt>
<parameters>
<parameter ismandatory="1">
<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>
<precond>
<code proglang="perl">defined $tree_file</code>
<code proglang="python">tree_file is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "U\\n" : ""</code>
<code proglang="python">( "" , "U\n")[ value ]</code>
</format>
<ctrl>
<message>
<text lang="en">You cannot randomize (jumble) your dataset and give a user tree at the same time</text>
</message>
<code proglang="perl">not ( $user_tree and $jumble )</code>
<code proglang="python">not ( user_tree and jumble )</code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">To give your tree to the program, you must normally put it in the alignment file, after the sequences, preceded by a line indicating how many trees you give.</text>
<text lang="en">Here, this will be automatically appended: just give a treefile and the number of trees in it.</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>tree_file</name>
<prompt lang="en">User Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$user_tree</code>
<code proglang="python">user_tree</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? "cat $tree_file >> intree; " : ""</code>
<code proglang="python">("" , "cat "+str( tree_file ) + " >> intree; " )[ value is not None ]</code>
</format>
<argpos>-1</argpos>
</parameter>
<parameter>
<name>use_lengths</name>
<prompt lang="en">Use lengths from user trees (N)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$user_tree</code>
<code proglang="python">user_tree</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "N\\n" : ""</code>
<code proglang="python">( "" , "N\n" )[ value ]</code>
</format>
<argpos>2</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>print_tree</name>
<prompt lang="en">Print out tree (3)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($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>fitch.params</paramfile>
</parameter>
<parameter>
<name>print_treefile</name>
<prompt lang="en">Write out trees onto tree file (4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : "4\\n"</code>
<code proglang="python">( "4\n" , "" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas).</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>printdata</name>
<prompt lang="en">Print out the data at start of run (1)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "1\\n" : ""</code>
<code proglang="python">( "" , "1\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>fitch.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 root (O)</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">$value > 0</code>
<code proglang="python">value > 0</code>
</ctrl>
<argpos>1</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>triangular</name>
<prompt lang="en">Matrix format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>square</value>
</vdef>
<flist>
<felem>
<value>square</value>
<label>Square</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>lower</value>
<label>Lower-triangular</label>
<code proglang="perl">"L\\n"</code>
<code proglang="python">"L\n"</code>
</felem>
<felem>
<value>upper</value>
<label>Upper-triangular</label>
<code proglang="perl">"R\\n"</code>
<code proglang="python">"R\n"</code>
</felem>
</flist>
<argpos>1</argpos>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>subreplicates</name>
<prompt lang="en">Subreplicates (S)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "S\\n" : ""</code>
<code proglang="python">( "" , "S\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">If the S (subreplication) option is in effect, the above degrees of freedom must be modified by noting that N is not n(n-1)/2 but is the sum of the numbers of replicates of all cells in the distance matrix read in, which may be either square or triangular. A further explanation of the statistical test of the clock is given in a paper of mine (Felsenstein, 1986).</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
<parameter>
<name>global</name>
<prompt lang="en">Global rearrangements (G)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "G\\n" : ""</code>
<code proglang="python">( "", "G\n")[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">is the Global search option. This causes, after the last species is added to the tree, each possible group to be removed and re-added. This improves the result, since the position of every species is reconsidered. It approximately triples the run-time of the program. It is not an option in KITSCH because it is the default and is always in force there.</text>
</comment>
<paramfile>fitch.params</paramfile>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt>Fitch output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" && mv outfile fitch.outfile"</code>
<code proglang="python">" && mv outfile fitch.outfile"</code>
</format>
<filenames>
<code proglang="perl">"fitch.outfile"</code>
<code proglang="python">"fitch.outfile"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>treefile</name>
<prompt>Fitch tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$print_treefile</code>
<code proglang="python">print_treefile</code>
</precond>
<format>
<code proglang="perl">" && mv outtree fitch.outtree"</code>
<code proglang="python">" && mv outtree fitch.outtree"</code>
</format>
<filenames>
<code proglang="perl">"fitch.outtree"</code>
<code proglang="python">"fitch.outtree"</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>fitch.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>fitch.params</paramfile>
</parameter>
</parameters>
</program>
|