1 <html xmlns:v="urn:schemas-microsoft-com:vml"
2 xmlns:o="urn:schemas-microsoft-com:office:office"
3 xmlns:w="urn:schemas-microsoft-com:office:word"
4 xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"
5 xmlns:css="http://macVmlSchemaUri" xmlns="http://www.w3.org/TR/REC-html40">
8 <meta name=Title content=Manual>
9 <meta name=Keywords content="">
10 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
11 <meta name=ProgId content=Word.Document>
12 <meta name=Generator content="Microsoft Word 2008">
13 <meta name=Originator content="Microsoft Word 2008">
14 <link rel=File-List href="t_coffee_technical_files/filelist.xml">
15 <link rel=Edit-Time-Data href="t_coffee_technical_files/editdata.mso">
18 v\:* {behavior:url(#default#VML);}
19 o\:* {behavior:url(#default#VML);}
20 w\:* {behavior:url(#default#VML);}
21 .shape {behavior:url(#default#VML);}
25 <!--[if gte mso 9]><xml>
26 <o:DocumentProperties>
27 <o:Author>Notredame</o:Author>
28 <o:Template>Normal.dotm</o:Template>
29 <o:LastAuthor>Notredame Cédric</o:LastAuthor>
30 <o:Revision>2</o:Revision>
31 <o:TotalTime>28629</o:TotalTime>
32 <o:LastPrinted>2006-03-05T19:42:00Z</o:LastPrinted>
33 <o:Created>2010-11-18T19:37:00Z</o:Created>
34 <o:LastSaved>2010-11-18T19:37:00Z</o:LastSaved>
36 <o:Words>18210</o:Words>
37 <o:Characters>103800</o:Characters>
38 <o:Company>SIB</o:Company>
39 <o:Lines>865</o:Lines>
40 <o:Paragraphs>207</o:Paragraphs>
41 <o:CharactersWithSpaces>127473</o:CharactersWithSpaces>
42 <o:Version>12.0</o:Version>
43 </o:DocumentProperties>
44 <o:OfficeDocumentSettings>
45 <o:PixelsPerInch>96</o:PixelsPerInch>
46 <o:TargetScreenSize>800x600</o:TargetScreenSize>
47 </o:OfficeDocumentSettings>
48 </xml><![endif]--><!--[if gte mso 9]><xml>
50 <w:TrackMoves>false</w:TrackMoves>
52 <w:HyphenationZone>21</w:HyphenationZone>
53 <w:ValidateAgainstSchemas/>
54 <w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
55 <w:IgnoreMixedContent>false</w:IgnoreMixedContent>
56 <w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
58 <w:BreakWrappedTables/>
59 <w:UseNormalStyleForList/>
60 <w:DontUseIndentAsNumberingTabStop/>
63 <w:DontAutofitConstrainedTables/>
65 <w:HangulWidthLikeWW11/>
68 </xml><![endif]--><!--[if gte mso 9]><xml>
69 <w:LatentStyles DefLockedState="false" LatentStyleCount="276">
74 /* Font Definitions */
77 panose-1:2 11 6 4 2 2 2 2 2 4;
79 mso-generic-font-family:auto;
80 mso-font-pitch:variable;
81 mso-font-signature:3 0 0 0 1 0;}
83 {font-family:"Courier New";
84 panose-1:2 7 3 9 2 2 5 2 4 4;
86 mso-generic-font-family:auto;
87 mso-font-pitch:variable;
88 mso-font-signature:3 0 0 0 1 0;}
91 panose-1:2 0 5 0 0 0 0 0 0 0;
93 mso-generic-font-family:auto;
94 mso-font-pitch:variable;
95 mso-font-signature:3 0 0 0 1 0;}
98 panose-1:2 11 5 3 3 4 4 4 2 4;
100 mso-generic-font-family:auto;
101 mso-font-pitch:variable;
102 mso-font-signature:3 0 0 0 1 0;}
104 {font-family:"Tms Rmn";
105 panose-1:0 0 0 0 0 0 0 0 0 0;
107 mso-generic-font-family:roman;
108 mso-font-format:other;
109 mso-font-pitch:variable;
110 mso-font-signature:3 0 0 0 1 0;}
113 panose-1:0 0 0 0 0 0 0 0 0 0;
115 mso-generic-font-family:swiss;
116 mso-font-format:other;
117 mso-font-pitch:variable;
118 mso-font-signature:3 0 0 0 1 0;}
120 {font-family:"MS Serif";
121 panose-1:0 0 0 0 0 0 0 0 0 0;
123 mso-generic-font-family:roman;
124 mso-font-format:other;
125 mso-font-pitch:variable;
126 mso-font-signature:3 0 0 0 1 0;}
128 {font-family:"MS Sans Serif";
129 panose-1:0 0 0 0 0 0 0 0 0 0;
131 mso-generic-font-family:swiss;
132 mso-font-format:other;
133 mso-font-pitch:variable;
134 mso-font-signature:3 0 0 0 1 0;}
136 {font-family:"New York";
137 panose-1:0 0 0 0 0 0 0 0 0 0;
139 mso-generic-font-family:roman;
140 mso-font-format:other;
141 mso-font-pitch:variable;
142 mso-font-signature:3 0 0 0 1 0;}
145 panose-1:0 0 0 0 0 0 0 0 0 0;
147 mso-generic-font-family:swiss;
148 mso-font-format:other;
149 mso-font-pitch:variable;
150 mso-font-signature:3 0 0 0 1 0;}
152 {font-family:Wingdings;
153 panose-1:5 2 1 2 1 8 4 8 7 8;
155 mso-generic-font-family:auto;
156 mso-font-pitch:variable;
157 mso-font-signature:0 0 65536 0 -2147483648 0;}
159 {font-family:"MS Mincho";
161 mso-generic-font-family:auto;
162 mso-font-pitch:variable;
163 mso-font-signature:1 0 16778247 0 131072 0;}
167 mso-generic-font-family:auto;
168 mso-font-pitch:variable;
169 mso-font-signature:1 0 16786438 0 524288 0;}
173 mso-generic-font-family:auto;
174 mso-font-pitch:variable;
175 mso-font-signature:1 0 16778254 0 262144 0;}
177 {font-family:PMingLiU;
179 mso-generic-font-family:auto;
180 mso-font-pitch:variable;
181 mso-font-signature:1 0 16778248 0 1048576 0;}
183 {font-family:"MS Gothic";
185 mso-generic-font-family:auto;
186 mso-font-pitch:variable;
187 mso-font-signature:1 0 16778247 0 131072 0;}
189 {font-family:Century;
190 panose-1:2 4 6 4 5 5 5 2 3 4;
192 mso-generic-font-family:auto;
193 mso-font-pitch:variable;
194 mso-font-signature:3 0 0 0 1 0;}
196 {font-family:Verdana;
197 panose-1:2 11 6 4 3 5 4 4 2 4;
199 mso-generic-font-family:auto;
200 mso-font-pitch:variable;
201 mso-font-signature:3 0 0 0 1 0;}
203 {font-family:Calibri;
204 panose-1:2 15 5 2 2 2 4 3 2 4;
206 mso-generic-font-family:auto;
207 mso-font-pitch:variable;
208 mso-font-signature:3 0 0 0 1 0;}
210 {font-family:Cambria;
211 panose-1:2 4 5 3 5 4 6 3 2 4;
213 mso-generic-font-family:auto;
214 mso-font-pitch:variable;
215 mso-font-signature:3 0 0 0 1 0;}
217 {font-family:"Cambria Math";
218 panose-1:0 0 0 0 0 0 0 0 0 0;
220 mso-generic-font-family:roman;
221 mso-font-format:other;
223 mso-font-signature:3 0 0 0 1 0;}
226 panose-1:2 11 6 4 3 5 4 4 2 4;
228 mso-generic-font-family:auto;
229 mso-font-pitch:variable;
230 mso-font-signature:3 0 0 0 1 0;}
232 {font-family:"MS Mincho";
233 mso-font-alt:"MS Mincho";
234 mso-font-charset:128;
235 mso-generic-font-family:modern;
236 mso-font-pitch:fixed;
237 mso-font-signature:-536870145 1791491579 18 0 131231 0;}
239 {font-family:PMingLiU;
240 mso-font-alt:PMingLiU;
241 mso-font-charset:136;
242 mso-generic-font-family:roman;
243 mso-font-pitch:variable;
244 mso-font-signature:-1610611969 684719354 22 0 1048577 0;}
246 {font-family:"Trebuchet MS";
247 panose-1:2 11 6 3 2 2 2 2 2 4;
249 mso-generic-font-family:auto;
250 mso-font-pitch:variable;
251 mso-font-signature:3 0 0 0 1 0;}
253 {font-family:"Century Schoolbook";
254 panose-1:2 4 6 4 5 5 5 2 3 4;
256 mso-generic-font-family:auto;
257 mso-font-pitch:variable;
258 mso-font-signature:3 0 0 0 1 0;}
260 {font-family:"Wingdings 2";
261 panose-1:5 2 1 2 1 5 7 7 7 7;
263 mso-generic-font-family:auto;
264 mso-font-pitch:variable;
265 mso-font-signature:0 0 65536 0 -2147483648 0;}
268 panose-1:2 11 8 6 3 9 2 5 2 4;
270 mso-generic-font-family:auto;
271 mso-font-pitch:variable;
272 mso-font-signature:3 0 0 0 1 0;}
274 {font-family:"Arial Black";
275 panose-1:2 11 10 4 2 1 2 2 2 4;
277 mso-generic-font-family:auto;
278 mso-font-pitch:variable;
279 mso-font-signature:3 0 0 0 1 0;}
281 {font-family:"Abadi MT Condensed Extra Bold";
282 panose-1:2 11 10 6 3 1 1 1 1 3;
284 mso-generic-font-family:auto;
285 mso-font-pitch:variable;
286 mso-font-signature:3 0 0 0 1 0;}
288 {font-family:"Abadi MT Condensed Light";
289 panose-1:2 11 3 6 3 1 1 1 1 3;
291 mso-generic-font-family:auto;
292 mso-font-pitch:variable;
293 mso-font-signature:3 0 0 0 1 0;}
295 {font-family:"American Typewriter";
296 panose-1:2 9 6 4 2 0 4 2 3 4;
298 mso-generic-font-family:auto;
299 mso-font-pitch:variable;
300 mso-font-signature:3 0 0 0 1 0;}
302 {font-family:"American Typewriter Condensed";
303 panose-1:2 9 6 6 2 0 4 2 3 4;
305 mso-generic-font-family:auto;
306 mso-font-pitch:variable;
307 mso-font-signature:3 0 0 0 1 0;}
309 {font-family:"American Typewriter Light";
310 panose-1:2 9 3 4 2 0 4 2 3 4;
312 mso-generic-font-family:auto;
313 mso-font-pitch:variable;
314 mso-font-signature:3 0 0 0 1 0;}
316 {font-family:"Andale Mono";
317 panose-1:2 11 5 9 0 0 0 0 0 4;
319 mso-generic-font-family:auto;
320 mso-font-pitch:variable;
321 mso-font-signature:3 0 0 0 1 0;}
323 {font-family:"Apple Casual";
324 panose-1:0 1 4 0 0 0 0 0 0 0;
326 mso-generic-font-family:auto;
327 mso-font-pitch:variable;
328 mso-font-signature:3 0 0 0 1 0;}
330 {font-family:"Apple Chancery";
331 panose-1:3 2 7 2 4 5 6 6 5 4;
333 mso-generic-font-family:auto;
334 mso-font-pitch:variable;
335 mso-font-signature:3 0 0 0 1 0;}
337 {font-family:"Apple Symbols";
338 panose-1:2 0 0 0 0 0 0 0 0 0;
340 mso-generic-font-family:auto;
341 mso-font-pitch:variable;
342 mso-font-signature:3 0 0 0 1 0;}
344 {font-family:"Arial Bold";
345 panose-1:2 11 7 4 2 2 2 2 2 4;
347 mso-generic-font-family:auto;
348 mso-font-pitch:variable;
349 mso-font-signature:3 0 0 0 1 0;}
351 {font-family:"Arial Italic";
352 panose-1:2 11 6 4 2 2 2 9 2 4;
354 mso-generic-font-family:auto;
355 mso-font-pitch:variable;
356 mso-font-signature:3 0 0 0 1 0;}
358 {font-family:"Arial Narrow";
359 panose-1:2 11 5 6 2 2 2 3 2 4;
361 mso-generic-font-family:auto;
362 mso-font-pitch:variable;
363 mso-font-signature:3 0 0 0 1 0;}
365 {font-family:"Arial Narrow Bold";
366 panose-1:2 11 7 6 2 2 2 3 2 4;
368 mso-generic-font-family:auto;
369 mso-font-pitch:variable;
370 mso-font-signature:3 0 0 0 1 0;}
372 {font-family:"Arial Narrow Bold Italic";
373 panose-1:2 11 7 6 2 2 2 10 2 4;
375 mso-generic-font-family:auto;
376 mso-font-pitch:variable;
377 mso-font-signature:3 0 0 0 1 0;}
379 {font-family:"Arial Narrow Italic";
380 panose-1:2 11 6 6 2 2 2 10 2 4;
382 mso-generic-font-family:auto;
383 mso-font-pitch:variable;
384 mso-font-signature:3 0 0 0 1 0;}
386 {font-family:"Arial Rounded MT Bold";
387 panose-1:2 15 7 4 3 5 4 3 2 4;
389 mso-generic-font-family:auto;
390 mso-font-pitch:variable;
391 mso-font-signature:3 0 0 0 1 0;}
393 {font-family:"Arial Unicode MS";
394 panose-1:2 11 6 4 2 2 2 2 2 4;
396 mso-generic-font-family:auto;
397 mso-font-pitch:variable;
398 mso-font-signature:3 0 0 0 1 0;}
400 {font-family:Ayuthaya;
401 panose-1:0 0 4 0 0 0 0 0 0 0;
403 mso-generic-font-family:auto;
404 mso-font-pitch:variable;
405 mso-font-signature:3 0 0 0 1 0;}
407 {font-family:Baskerville;
408 panose-1:2 2 5 2 7 4 1 2 3 3;
410 mso-generic-font-family:auto;
411 mso-font-pitch:variable;
412 mso-font-signature:3 0 0 0 1 0;}
414 {font-family:"Baskerville Old Face";
415 panose-1:2 2 6 2 8 5 5 2 3 3;
417 mso-generic-font-family:auto;
418 mso-font-pitch:variable;
419 mso-font-signature:3 0 0 0 1 0;}
421 {font-family:"Baskerville Semibold";
422 panose-1:2 2 7 2 7 4 0 2 2 3;
424 mso-generic-font-family:auto;
425 mso-font-pitch:variable;
426 mso-font-signature:3 0 0 0 1 0;}
428 {font-family:"Bauhaus 93";
429 panose-1:4 3 9 5 2 11 2 2 12 2;
431 mso-generic-font-family:auto;
432 mso-font-pitch:variable;
433 mso-font-signature:3 0 0 0 1 0;}
435 {font-family:"Bell MT";
436 panose-1:2 2 5 3 6 3 5 2 3 3;
438 mso-generic-font-family:auto;
439 mso-font-pitch:variable;
440 mso-font-signature:3 0 0 0 1 0;}
442 {font-family:"Bernard MT Condensed";
443 panose-1:2 5 8 6 6 9 5 2 4 4;
445 mso-generic-font-family:auto;
446 mso-font-pitch:variable;
447 mso-font-signature:3 0 0 0 1 0;}
449 {font-family:"Big Caslon";
450 panose-1:2 0 6 3 9 0 0 2 0 3;
452 mso-generic-font-family:auto;
453 mso-font-pitch:variable;
454 mso-font-signature:3 0 0 0 1 0;}
456 {font-family:"BlairMdITC TT-Medium";
457 panose-1:0 0 5 0 0 0 0 0 0 0;
459 mso-generic-font-family:auto;
460 mso-font-pitch:variable;
461 mso-font-signature:3 0 0 0 1 0;}
463 {font-family:"Book Antiqua";
464 panose-1:2 4 6 2 5 3 5 3 3 4;
466 mso-generic-font-family:auto;
467 mso-font-pitch:variable;
468 mso-font-signature:3 0 0 0 1 0;}
470 {font-family:"Bookman Old Style";
471 panose-1:2 5 6 4 5 5 5 2 2 4;
473 mso-generic-font-family:auto;
474 mso-font-pitch:variable;
475 mso-font-signature:3 0 0 0 1 0;}
477 {font-family:"Bookshelf Symbol 7";
478 panose-1:5 1 1 1 1 1 1 1 1 1;
480 mso-generic-font-family:auto;
481 mso-font-pitch:variable;
482 mso-font-signature:3 0 0 0 1 0;}
484 {font-family:"Bordeaux Roman Bold LET";
485 panose-1:2 0 5 0 0 0 0 0 0 0;
487 mso-generic-font-family:auto;
488 mso-font-pitch:variable;
489 mso-font-signature:3 0 0 0 1 0;}
491 {font-family:Braggadocio;
492 panose-1:4 3 11 7 13 11 2 2 4 3;
494 mso-generic-font-family:auto;
495 mso-font-pitch:variable;
496 mso-font-signature:3 0 0 0 1 0;}
498 {font-family:"Britannic Bold";
499 panose-1:2 11 9 3 6 7 3 2 2 4;
501 mso-generic-font-family:auto;
502 mso-font-pitch:variable;
503 mso-font-signature:3 0 0 0 1 0;}
505 {font-family:"Brush Script MT Italic";
506 panose-1:3 6 8 2 4 4 6 7 3 4;
508 mso-generic-font-family:auto;
509 mso-font-pitch:variable;
510 mso-font-signature:3 0 0 0 1 0;}
512 {font-family:"Calisto MT";
513 panose-1:2 4 6 3 5 5 5 3 3 4;
515 mso-generic-font-family:auto;
516 mso-font-pitch:variable;
517 mso-font-signature:3 0 0 0 1 0;}
519 {font-family:Candara;
520 panose-1:2 14 5 2 3 3 3 2 2 4;
522 mso-generic-font-family:auto;
523 mso-font-pitch:variable;
524 mso-font-signature:3 0 0 0 1 0;}
526 {font-family:"Century Gothic";
527 panose-1:2 11 5 2 2 2 2 2 2 4;
529 mso-generic-font-family:auto;
530 mso-font-pitch:variable;
531 mso-font-signature:3 0 0 0 1 0;}
533 {font-family:Chalkboard;
534 panose-1:3 5 6 2 4 2 2 2 2 5;
536 mso-generic-font-family:auto;
537 mso-font-pitch:variable;
538 mso-font-signature:3 0 0 0 1 0;}
540 {font-family:Chalkduster;
541 panose-1:3 5 6 2 4 2 2 2 2 5;
543 mso-generic-font-family:auto;
544 mso-font-pitch:variable;
545 mso-font-signature:3 0 0 0 1 0;}
548 panose-1:2 0 6 3 2 0 0 2 0 3;
550 mso-generic-font-family:auto;
551 mso-font-pitch:variable;
552 mso-font-signature:3 0 0 0 1 0;}
554 {font-family:"Colonna MT";
555 panose-1:4 2 8 5 6 2 2 3 2 3;
557 mso-generic-font-family:auto;
558 mso-font-pitch:variable;
559 mso-font-signature:3 0 0 0 1 0;}
561 {font-family:"Comic Sans MS";
562 panose-1:3 15 7 2 3 3 2 2 2 4;
564 mso-generic-font-family:auto;
565 mso-font-pitch:variable;
566 mso-font-signature:3 0 0 0 1 0;}
568 {font-family:"Comic Sans MS Bold";
569 panose-1:3 15 9 2 3 3 2 2 2 4;
571 mso-generic-font-family:auto;
572 mso-font-pitch:variable;
573 mso-font-signature:3 0 0 0 1 0;}
575 {font-family:Consolas;
576 panose-1:2 11 6 9 2 2 4 3 2 4;
578 mso-generic-font-family:auto;
579 mso-font-pitch:variable;
580 mso-font-signature:3 0 0 0 1 0;}
582 {font-family:Constantia;
583 panose-1:2 3 6 2 5 3 6 3 3 3;
585 mso-generic-font-family:auto;
586 mso-font-pitch:variable;
587 mso-font-signature:3 0 0 0 1 0;}
589 {font-family:"Cooper Black";
590 panose-1:2 8 9 4 4 3 11 2 4 4;
592 mso-generic-font-family:auto;
593 mso-font-pitch:variable;
594 mso-font-signature:3 0 0 0 1 0;}
596 {font-family:Copperplate;
597 panose-1:2 0 5 4 0 0 0 2 0 4;
599 mso-generic-font-family:auto;
600 mso-font-pitch:variable;
601 mso-font-signature:3 0 0 0 1 0;}
603 {font-family:"Copperplate Gothic Bold";
604 panose-1:2 14 7 5 2 2 6 2 4 4;
606 mso-generic-font-family:auto;
607 mso-font-pitch:variable;
608 mso-font-signature:3 0 0 0 1 0;}
610 {font-family:"Copperplate Gothic Light";
611 panose-1:2 14 5 7 2 2 6 2 4 4;
613 mso-generic-font-family:auto;
614 mso-font-pitch:variable;
615 mso-font-signature:3 0 0 0 1 0;}
617 {font-family:"Copperplate Light";
618 panose-1:2 0 6 4 3 0 0 2 0 4;
620 mso-generic-font-family:auto;
621 mso-font-pitch:variable;
622 mso-font-signature:3 0 0 0 1 0;}
625 panose-1:2 11 5 3 2 2 4 2 2 4;
627 mso-generic-font-family:auto;
628 mso-font-pitch:variable;
629 mso-font-signature:3 0 0 0 1 0;}
631 {font-family:Cracked;
632 panose-1:0 0 4 0 0 0 0 0 0 0;
634 mso-generic-font-family:auto;
635 mso-font-pitch:variable;
636 mso-font-signature:3 0 0 0 1 0;}
638 {font-family:"Curlz MT";
639 panose-1:4 4 4 4 5 7 2 2 2 2;
641 mso-generic-font-family:auto;
642 mso-font-pitch:variable;
643 mso-font-signature:3 0 0 0 1 0;}
645 {font-family:Desdemona;
646 panose-1:4 2 5 5 2 14 3 4 5 4;
648 mso-generic-font-family:auto;
649 mso-font-pitch:variable;
650 mso-font-signature:3 0 0 0 1 0;}
653 panose-1:2 0 5 3 0 0 0 2 0 3;
655 mso-generic-font-family:auto;
656 mso-font-pitch:variable;
657 mso-font-signature:3 0 0 0 1 0;}
659 {font-family:"Edwardian Script ITC";
660 panose-1:3 3 3 2 4 7 7 13 8 4;
662 mso-generic-font-family:auto;
663 mso-font-pitch:variable;
664 mso-font-signature:3 0 0 0 1 0;}
666 {font-family:"Engravers MT";
667 panose-1:2 9 7 7 8 5 5 2 3 4;
669 mso-generic-font-family:auto;
670 mso-font-pitch:variable;
671 mso-font-signature:3 0 0 0 1 0;}
673 {font-family:"Euphemia UCAS";
674 panose-1:2 11 5 3 4 1 2 2 1 4;
676 mso-generic-font-family:auto;
677 mso-font-pitch:variable;
678 mso-font-signature:3 0 0 0 1 0;}
680 {font-family:Eurostile;
681 panose-1:2 11 5 4 2 2 2 5 2 4;
683 mso-generic-font-family:auto;
684 mso-font-pitch:variable;
685 mso-font-signature:3 0 0 0 1 0;}
687 {font-family:"Footlight MT Light";
688 panose-1:2 4 6 2 6 3 10 2 3 4;
690 mso-generic-font-family:auto;
691 mso-font-pitch:variable;
692 mso-font-signature:3 0 0 0 1 0;}
694 {font-family:"Franklin Gothic Book";
695 panose-1:2 11 5 3 2 1 2 2 2 4;
697 mso-generic-font-family:auto;
698 mso-font-pitch:variable;
699 mso-font-signature:3 0 0 0 1 0;}
701 {font-family:"Franklin Gothic Medium";
702 panose-1:2 11 6 3 2 1 2 2 2 4;
704 mso-generic-font-family:auto;
705 mso-font-pitch:variable;
706 mso-font-signature:3 0 0 0 1 0;}
709 panose-1:2 11 6 2 2 2 4 2 3 3;
711 mso-generic-font-family:auto;
712 mso-font-pitch:variable;
713 mso-font-signature:3 0 0 0 1 0;}
715 {font-family:"Futura Condensed";
716 panose-1:2 11 5 6 2 2 4 3 2 4;
718 mso-generic-font-family:auto;
719 mso-font-pitch:variable;
720 mso-font-signature:3 0 0 0 1 0;}
722 {font-family:Garamond;
723 panose-1:2 2 4 4 3 3 1 1 8 3;
725 mso-generic-font-family:auto;
726 mso-font-pitch:variable;
727 mso-font-signature:3 0 0 0 1 0;}
729 {font-family:Georgia;
730 panose-1:2 4 5 2 5 4 5 2 3 3;
732 mso-generic-font-family:auto;
733 mso-font-pitch:variable;
734 mso-font-signature:3 0 0 0 1 0;}
736 {font-family:"Gill Sans";
737 panose-1:2 11 5 2 2 1 4 2 2 3;
739 mso-generic-font-family:auto;
740 mso-font-pitch:variable;
741 mso-font-signature:3 0 0 0 1 0;}
743 {font-family:"Gill Sans Light";
744 panose-1:2 11 3 2 2 1 4 2 2 3;
746 mso-generic-font-family:auto;
747 mso-font-pitch:variable;
748 mso-font-signature:3 0 0 0 1 0;}
750 {font-family:"Gill Sans MT";
751 panose-1:2 11 5 2 2 1 4 2 2 3;
753 mso-generic-font-family:auto;
754 mso-font-pitch:variable;
755 mso-font-signature:3 0 0 0 1 0;}
757 {font-family:"Gill Sans Ultra Bold";
758 panose-1:2 11 10 2 2 1 4 2 2 3;
760 mso-generic-font-family:auto;
761 mso-font-pitch:variable;
762 mso-font-signature:3 0 0 0 1 0;}
764 {font-family:"Gloucester MT Extra Condensed";
765 panose-1:2 3 8 8 2 6 1 1 1 1;
767 mso-generic-font-family:auto;
768 mso-font-pitch:variable;
769 mso-font-signature:3 0 0 0 1 0;}
771 {font-family:"Goudy Old Style";
772 panose-1:2 2 5 2 5 3 5 2 3 3;
774 mso-generic-font-family:auto;
775 mso-font-pitch:variable;
776 mso-font-signature:3 0 0 0 1 0;}
778 {font-family:Haettenschweiler;
779 panose-1:2 11 7 6 4 9 2 6 2 4;
781 mso-generic-font-family:auto;
782 mso-font-pitch:variable;
783 mso-font-signature:3 0 0 0 1 0;}
785 {font-family:"Handwriting - Dakota";
786 panose-1:2 0 4 0 0 0 0 0 0 0;
788 mso-generic-font-family:auto;
789 mso-font-pitch:variable;
790 mso-font-signature:3 0 0 0 1 0;}
792 {font-family:Harrington;
793 panose-1:4 4 5 5 5 10 2 2 7 2;
795 mso-generic-font-family:auto;
796 mso-font-pitch:variable;
797 mso-font-signature:3 0 0 0 1 0;}
799 {font-family:"Helvetica Neue";
800 panose-1:2 0 5 3 0 0 0 2 0 4;
802 mso-generic-font-family:auto;
803 mso-font-pitch:variable;
804 mso-font-signature:3 0 0 0 1 0;}
806 {font-family:"Helvetica Neue Black Condensed";
807 panose-1:2 0 10 6 0 0 0 2 0 4;
809 mso-generic-font-family:auto;
810 mso-font-pitch:variable;
811 mso-font-signature:3 0 0 0 1 0;}
813 {font-family:"Helvetica Neue Bold Condensed";
814 panose-1:2 0 8 6 0 0 0 2 0 4;
816 mso-generic-font-family:auto;
817 mso-font-pitch:variable;
818 mso-font-signature:3 0 0 0 1 0;}
820 {font-family:"Helvetica Neue Light";
821 panose-1:2 0 4 3 0 0 0 2 0 4;
823 mso-generic-font-family:auto;
824 mso-font-pitch:variable;
825 mso-font-signature:3 0 0 0 1 0;}
827 {font-family:"Helvetica Neue Medium";
828 panose-1:2 11 6 4 2 2 2 2 2 4;
830 mso-generic-font-family:auto;
831 mso-font-pitch:variable;
832 mso-font-signature:3 0 0 0 1 0;}
834 {font-family:"Helvetica Neue UltraLight";
835 panose-1:2 0 2 6 0 0 0 2 0 4;
837 mso-generic-font-family:auto;
838 mso-font-pitch:variable;
839 mso-font-signature:3 0 0 0 1 0;}
841 {font-family:Herculanum;
842 panose-1:2 0 5 5 0 0 0 2 0 4;
844 mso-generic-font-family:auto;
845 mso-font-pitch:variable;
846 mso-font-signature:3 0 0 0 1 0;}
848 {font-family:"Hoefler Text";
849 panose-1:2 3 6 2 5 5 6 2 2 3;
851 mso-generic-font-family:auto;
852 mso-font-pitch:variable;
853 mso-font-signature:3 0 0 0 1 0;}
855 {font-family:"Hoefler Text Ornaments";
856 panose-1:0 0 0 0 0 0 0 0 0 0;
858 mso-generic-font-family:auto;
859 mso-font-pitch:variable;
860 mso-font-signature:0 0 65536 0 -2147483648 0;}
862 {font-family:"Imprint MT Shadow";
863 panose-1:4 2 6 5 6 3 3 3 2 2;
865 mso-generic-font-family:auto;
866 mso-font-pitch:variable;
867 mso-font-signature:3 0 0 0 1 0;}
869 {font-family:InaiMathi;
870 panose-1:2 0 5 0 0 0 0 0 0 0;
872 mso-generic-font-family:auto;
873 mso-font-pitch:variable;
874 mso-font-signature:3 0 0 0 1 0;}
876 {font-family:"Kino MT";
877 panose-1:4 3 7 5 13 12 2 2 7 3;
879 mso-generic-font-family:auto;
880 mso-font-pitch:variable;
881 mso-font-signature:3 0 0 0 1 0;}
883 {font-family:Krungthep;
884 panose-1:2 0 4 0 0 0 0 0 0 0;
886 mso-generic-font-family:auto;
887 mso-font-pitch:variable;
888 mso-font-signature:3 0 0 0 1 0;}
890 {font-family:KufiStandardGK;
891 panose-1:0 0 4 0 0 0 0 0 0 0;
893 mso-generic-font-family:auto;
894 mso-font-pitch:variable;
895 mso-font-signature:3 0 0 0 1 0;}
897 {font-family:"Lucida Blackletter";
898 panose-1:0 0 0 0 0 0 0 0 0 0;
900 mso-generic-font-family:auto;
901 mso-font-pitch:variable;
902 mso-font-signature:3 0 0 0 1 0;}
904 {font-family:"Lucida Bright";
905 panose-1:2 4 6 2 5 5 5 2 3 4;
907 mso-generic-font-family:auto;
908 mso-font-pitch:variable;
909 mso-font-signature:3 0 0 0 1 0;}
911 {font-family:"Lucida Calligraphy";
912 panose-1:3 1 1 1 1 1 1 1 1 1;
914 mso-generic-font-family:auto;
915 mso-font-pitch:variable;
916 mso-font-signature:3 0 0 0 1 0;}
918 {font-family:"Lucida Console";
919 panose-1:2 11 6 9 4 5 4 2 2 4;
921 mso-generic-font-family:auto;
922 mso-font-pitch:variable;
923 mso-font-signature:3 0 0 0 1 0;}
925 {font-family:"Lucida Fax";
926 panose-1:2 6 6 2 5 5 5 2 2 4;
928 mso-generic-font-family:auto;
929 mso-font-pitch:variable;
930 mso-font-signature:3 0 0 0 1 0;}
932 {font-family:"Lucida Grande";
934 mso-generic-font-family:auto;
935 mso-font-pitch:variable;
936 mso-font-signature:3 0 0 0 1 0;}
938 {font-family:"Lucida Handwriting";
939 panose-1:3 1 1 1 1 1 1 1 1 1;
941 mso-generic-font-family:auto;
942 mso-font-pitch:variable;
943 mso-font-signature:3 0 0 0 1 0;}
945 {font-family:"Lucida Sans";
946 panose-1:2 11 6 2 3 5 4 2 2 4;
948 mso-generic-font-family:auto;
949 mso-font-pitch:variable;
950 mso-font-signature:3 0 0 0 1 0;}
952 {font-family:"Lucida Sans Typewriter";
953 panose-1:2 11 5 9 3 5 4 3 2 4;
955 mso-generic-font-family:auto;
956 mso-font-pitch:variable;
957 mso-font-signature:3 0 0 0 1 0;}
959 {font-family:"Lucida Sans Unicode";
960 panose-1:2 11 6 2 3 5 4 2 2 4;
962 mso-generic-font-family:auto;
963 mso-font-pitch:variable;
964 mso-font-signature:3 0 0 0 1 0;}
966 {font-family:"Marker Felt";
967 panose-1:2 0 4 0 0 0 0 0 0 0;
969 mso-generic-font-family:auto;
970 mso-font-pitch:variable;
971 mso-font-signature:3 0 0 0 1 0;}
973 {font-family:Marlett;
974 panose-1:0 0 0 0 0 0 0 0 0 0;
976 mso-generic-font-family:auto;
977 mso-font-pitch:variable;
978 mso-font-signature:3 0 0 0 1 0;}
980 {font-family:"Matura MT Script Capitals";
981 panose-1:3 2 8 2 6 6 2 7 2 2;
983 mso-generic-font-family:auto;
984 mso-font-pitch:variable;
985 mso-font-signature:3 0 0 0 1 0;}
987 {font-family:"Menlo Bold";
988 panose-1:2 11 7 9 3 6 4 2 2 4;
990 mso-generic-font-family:auto;
991 mso-font-pitch:variable;
992 mso-font-signature:3 0 0 0 1 0;}
994 {font-family:"Menlo Bold Italic";
995 panose-1:2 11 7 9 3 3 4 11 2 4;
997 mso-generic-font-family:auto;
998 mso-font-pitch:variable;
999 mso-font-signature:3 0 0 0 1 0;}
1001 {font-family:"Menlo Italic";
1002 panose-1:2 11 6 9 3 3 4 11 2 4;
1004 mso-generic-font-family:auto;
1005 mso-font-pitch:variable;
1006 mso-font-signature:3 0 0 0 1 0;}
1008 {font-family:"Menlo Regular";
1009 panose-1:2 11 6 9 3 8 4 2 2 4;
1011 mso-generic-font-family:auto;
1012 mso-font-pitch:variable;
1013 mso-font-signature:3 0 0 0 1 0;}
1015 {font-family:"Microsoft Sans Serif";
1016 panose-1:2 11 6 4 2 2 2 2 2 4;
1018 mso-generic-font-family:auto;
1019 mso-font-pitch:variable;
1020 mso-font-signature:3 0 0 0 1 0;}
1022 {font-family:Mistral;
1023 panose-1:3 9 7 2 3 4 7 2 4 3;
1025 mso-generic-font-family:auto;
1026 mso-font-pitch:variable;
1027 mso-font-signature:3 0 0 0 1 0;}
1029 {font-family:"Modern No\. 20";
1030 panose-1:2 7 7 4 7 5 5 2 3 3;
1032 mso-generic-font-family:auto;
1033 mso-font-pitch:variable;
1034 mso-font-signature:3 0 0 0 1 0;}
1036 {font-family:Monaco;
1037 panose-1:2 0 5 0 0 0 0 0 0 0;
1039 mso-generic-font-family:auto;
1040 mso-font-pitch:variable;
1041 mso-font-signature:3 0 0 0 1 0;}
1043 {font-family:"Monotype Corsiva";
1044 panose-1:3 1 1 1 1 2 1 1 1 1;
1046 mso-generic-font-family:auto;
1047 mso-font-pitch:variable;
1048 mso-font-signature:3 0 0 0 1 0;}
1050 {font-family:"Monotype Sorts";
1051 panose-1:1 1 6 1 1 1 1 1 1 1;
1053 mso-generic-font-family:auto;
1054 mso-font-pitch:variable;
1055 mso-font-signature:0 0 65536 0 -2147483648 0;}
1057 {font-family:"MS Reference Sans Serif";
1058 panose-1:2 11 6 4 3 5 4 4 2 4;
1060 mso-generic-font-family:auto;
1061 mso-font-pitch:variable;
1062 mso-font-signature:3 0 0 0 1 0;}
1064 {font-family:"MS Reference Specialty";
1065 panose-1:5 0 5 0 0 0 0 0 0 0;
1067 mso-generic-font-family:auto;
1068 mso-font-pitch:variable;
1069 mso-font-signature:3 0 0 0 1 0;}
1071 {font-family:"MT Extra";
1072 panose-1:5 5 1 2 1 2 5 2 2 2;
1074 mso-generic-font-family:auto;
1075 mso-font-pitch:variable;
1076 mso-font-signature:0 0 65536 0 -2147483648 0;}
1078 {font-family:"News Gothic MT";
1079 panose-1:2 11 5 4 2 2 3 2 2 4;
1081 mso-generic-font-family:auto;
1082 mso-font-pitch:variable;
1083 mso-font-signature:3 0 0 0 1 0;}
1086 panose-1:4 5 6 2 8 7 2 2 2 3;
1088 mso-generic-font-family:auto;
1089 mso-font-pitch:variable;
1090 mso-font-signature:3 0 0 0 1 0;}
1092 {font-family:Optima;
1093 panose-1:2 0 5 3 6 0 0 2 0 4;
1095 mso-generic-font-family:auto;
1096 mso-font-pitch:variable;
1097 mso-font-signature:3 0 0 0 1 0;}
1099 {font-family:"Optima ExtraBlack";
1100 panose-1:2 0 11 3 0 0 0 2 0 4;
1102 mso-generic-font-family:auto;
1103 mso-font-pitch:variable;
1104 mso-font-signature:3 0 0 0 1 0;}
1106 {font-family:Palatino;
1107 panose-1:2 0 5 0 0 0 0 0 0 0;
1109 mso-generic-font-family:auto;
1110 mso-font-pitch:variable;
1111 mso-font-signature:3 0 0 0 1 0;}
1113 {font-family:Papyrus;
1114 panose-1:2 11 6 2 4 2 0 2 3 3;
1116 mso-generic-font-family:auto;
1117 mso-font-pitch:variable;
1118 mso-font-signature:3 0 0 0 1 0;}
1120 {font-family:"Papyrus Condensed";
1121 panose-1:2 11 6 2 4 2 0 2 3 3;
1123 mso-generic-font-family:auto;
1124 mso-font-pitch:variable;
1125 mso-font-signature:3 0 0 0 1 0;}
1127 {font-family:Perpetua;
1128 panose-1:2 2 5 2 6 4 1 2 3 3;
1130 mso-generic-font-family:auto;
1131 mso-font-pitch:variable;
1132 mso-font-signature:3 0 0 0 1 0;}
1134 {font-family:"Perpetua Titling MT";
1135 panose-1:2 2 5 2 6 5 5 2 8 4;
1137 mso-generic-font-family:auto;
1138 mso-font-pitch:variable;
1139 mso-font-signature:3 0 0 0 1 0;}
1141 {font-family:"Plantagenet Cherokee";
1142 panose-1:2 2 0 0 0 0 0 0 0 0;
1144 mso-generic-font-family:auto;
1145 mso-font-pitch:variable;
1146 mso-font-signature:3 0 0 0 1 0;}
1148 {font-family:Playbill;
1149 panose-1:4 5 6 3 10 6 2 2 2 2;
1151 mso-generic-font-family:auto;
1152 mso-font-pitch:variable;
1153 mso-font-signature:3 0 0 0 1 0;}
1155 {font-family:"PortagoITC TT";
1156 panose-1:0 0 4 0 0 0 0 0 0 0;
1158 mso-generic-font-family:auto;
1159 mso-font-pitch:variable;
1160 mso-font-signature:3 0 0 0 1 0;}
1162 {font-family:Rockwell;
1163 panose-1:2 6 6 3 2 2 5 2 4 3;
1165 mso-generic-font-family:auto;
1166 mso-font-pitch:variable;
1167 mso-font-signature:3 0 0 0 1 0;}
1169 {font-family:"Rockwell Extra Bold";
1170 panose-1:2 6 9 3 4 5 5 2 4 3;
1172 mso-generic-font-family:auto;
1173 mso-font-pitch:variable;
1174 mso-font-signature:3 0 0 0 1 0;}
1177 panose-1:0 0 4 0 0 0 0 0 0 0;
1179 mso-generic-font-family:auto;
1180 mso-font-pitch:variable;
1181 mso-font-signature:3 0 0 0 1 0;}
1184 panose-1:0 0 4 0 0 0 0 0 0 0;
1186 mso-generic-font-family:auto;
1187 mso-font-pitch:variable;
1188 mso-font-signature:3 0 0 0 1 0;}
1191 panose-1:2 13 5 2 2 2 4 2 2 4;
1193 mso-generic-font-family:auto;
1194 mso-font-pitch:variable;
1195 mso-font-signature:3 0 0 0 1 0;}
1197 {font-family:Stencil;
1198 panose-1:4 4 9 5 13 8 2 2 4 4;
1200 mso-generic-font-family:auto;
1201 mso-font-pitch:variable;
1202 mso-font-signature:3 0 0 0 1 0;}
1204 {font-family:"Tahoma Bold";
1205 panose-1:2 11 8 4 3 5 4 4 2 4;
1207 mso-generic-font-family:auto;
1208 mso-font-pitch:variable;
1209 mso-font-signature:3 0 0 0 1 0;}
1211 {font-family:Thonburi;
1212 panose-1:0 0 4 0 0 0 0 0 0 0;
1214 mso-generic-font-family:auto;
1215 mso-font-pitch:variable;
1216 mso-font-signature:3 0 0 0 1 0;}
1218 {font-family:"Times New Roman Bold Italic";
1219 panose-1:2 2 7 3 6 5 5 9 3 4;
1221 mso-generic-font-family:auto;
1222 mso-font-pitch:variable;
1223 mso-font-signature:3 0 0 0 1 0;}
1225 {font-family:"Trebuchet MS Bold";
1226 panose-1:2 11 7 3 2 2 2 2 2 4;
1228 mso-generic-font-family:auto;
1229 mso-font-pitch:variable;
1230 mso-font-signature:3 0 0 0 1 0;}
1232 {font-family:"Trebuchet MS Bold Italic";
1233 panose-1:2 11 7 3 2 2 2 9 2 4;
1235 mso-generic-font-family:auto;
1236 mso-font-pitch:variable;
1237 mso-font-signature:3 0 0 0 1 0;}
1239 {font-family:"Trebuchet MS Italic";
1240 panose-1:2 11 6 3 2 2 2 9 2 4;
1242 mso-generic-font-family:auto;
1243 mso-font-pitch:variable;
1244 mso-font-signature:3 0 0 0 1 0;}
1246 {font-family:"Tw Cen MT";
1247 panose-1:2 11 6 2 2 1 4 2 6 3;
1249 mso-generic-font-family:auto;
1250 mso-font-pitch:variable;
1251 mso-font-signature:3 0 0 0 1 0;}
1253 {font-family:Webdings;
1254 panose-1:5 3 1 2 1 5 9 6 7 3;
1256 mso-generic-font-family:auto;
1257 mso-font-pitch:variable;
1258 mso-font-signature:0 0 65536 0 -2147483648 0;}
1260 {font-family:"Wide Latin";
1261 panose-1:2 10 10 7 5 5 5 2 4 4;
1263 mso-generic-font-family:auto;
1264 mso-font-pitch:variable;
1265 mso-font-signature:3 0 0 0 1 0;}
1267 {font-family:"Wingdings 3";
1268 panose-1:5 4 1 2 1 8 7 7 7 7;
1270 mso-generic-font-family:auto;
1271 mso-font-pitch:variable;
1272 mso-font-signature:0 0 65536 0 -2147483648 0;}
1274 {font-family:"Zapf Dingbats";
1275 panose-1:5 2 1 2 1 7 4 2 6 9;
1277 mso-generic-font-family:auto;
1278 mso-font-pitch:variable;
1279 mso-font-signature:0 0 65536 0 -2147483648 0;}
1281 {font-family:Zapfino;
1282 panose-1:3 3 3 0 4 7 7 7 12 3;
1284 mso-generic-font-family:auto;
1285 mso-font-pitch:variable;
1286 mso-font-signature:3 0 0 0 1 0;}
1288 {font-family:"Lucida Grande CE";
1289 panose-1:2 11 6 0 4 5 2 2 2 4;
1290 mso-font-charset:88;
1291 mso-generic-font-family:auto;
1292 mso-font-pitch:variable;
1293 mso-font-signature:5 0 0 0 2 0;}
1295 {font-family:"Charcoal CY";
1296 panose-1:0 0 4 0 0 0 0 0 0 0;
1297 mso-font-charset:89;
1298 mso-generic-font-family:auto;
1299 mso-font-pitch:variable;
1300 mso-font-signature:513 0 0 0 4 0;}
1302 {font-family:"Geneva CY";
1303 panose-1:0 0 4 0 0 0 0 0 0 0;
1304 mso-font-charset:89;
1305 mso-generic-font-family:auto;
1306 mso-font-pitch:variable;
1307 mso-font-signature:513 0 0 0 4 0;}
1309 {font-family:"Helvetica CY";
1310 panose-1:0 0 4 0 0 0 0 0 0 0;
1311 mso-font-charset:89;
1312 mso-generic-font-family:auto;
1313 mso-font-pitch:variable;
1314 mso-font-signature:513 0 0 0 4 0;}
1316 {font-family:"Lucida Grande CY";
1317 panose-1:2 11 6 0 4 5 2 2 2 4;
1318 mso-font-charset:89;
1319 mso-generic-font-family:auto;
1320 mso-font-pitch:variable;
1321 mso-font-signature:513 0 0 0 4 0;}
1323 {font-family:"Apple LiGothic Medium";
1324 panose-1:2 0 5 0 0 0 0 0 0 0;
1325 mso-font-charset:81;
1326 mso-generic-font-family:auto;
1327 mso-font-pitch:variable;
1328 mso-font-signature:1 0 16778248 0 1048576 0;}
1330 {font-family:"Apple LiSung Light";
1331 panose-1:2 0 5 0 0 0 0 0 0 0;
1332 mso-font-charset:81;
1333 mso-generic-font-family:auto;
1334 mso-font-pitch:variable;
1335 mso-font-signature:1 0 16778248 0 1048576 0;}
1337 {font-family:BiauKai;
1338 panose-1:2 1 6 1 0 1 1 1 1 1;
1339 mso-font-charset:81;
1340 mso-generic-font-family:auto;
1341 mso-font-pitch:variable;
1342 mso-font-signature:1 0 16778248 0 1048576 0;}
1344 {font-family:"Heiti TC Light";
1345 panose-1:2 0 0 0 0 0 0 0 0 0;
1346 mso-font-charset:81;
1347 mso-generic-font-family:auto;
1348 mso-font-pitch:variable;
1349 mso-font-signature:1 0 16778248 0 1048576 0;}
1351 {font-family:"Heiti TC Medium";
1352 panose-1:0 0 0 0 0 0 0 0 0 0;
1353 mso-font-charset:81;
1354 mso-generic-font-family:auto;
1355 mso-font-pitch:variable;
1356 mso-font-signature:1 0 16778248 0 1048576 0;}
1358 {font-family:"\5137\5B8B Pro";
1359 mso-font-charset:81;
1360 mso-generic-font-family:auto;
1361 mso-font-pitch:variable;
1362 mso-font-signature:1 0 16778248 0 1048576 0;}
1364 {font-family:"\5137\9ED1 Pro";
1365 mso-font-charset:81;
1366 mso-generic-font-family:auto;
1367 mso-font-pitch:variable;
1368 mso-font-signature:1 0 16778248 0 1048576 0;}
1370 {font-family:"GB18030 Bitmap";
1371 mso-font-charset:80;
1372 mso-generic-font-family:auto;
1373 mso-font-pitch:variable;
1374 mso-font-signature:1 0 16778254 0 262144 0;}
1377 panose-1:2 0 5 0 0 0 0 0 0 0;
1378 mso-font-charset:80;
1379 mso-generic-font-family:auto;
1380 mso-font-pitch:variable;
1381 mso-font-signature:1 0 16778254 0 262144 0;}
1383 {font-family:"Heiti SC Light";
1384 panose-1:2 0 0 0 0 0 0 0 0 0;
1385 mso-font-charset:80;
1386 mso-generic-font-family:auto;
1387 mso-font-pitch:variable;
1388 mso-font-signature:1 0 16778254 0 262144 0;}
1390 {font-family:"Heiti SC Medium";
1391 panose-1:0 0 0 0 0 0 0 0 0 0;
1392 mso-font-charset:80;
1393 mso-generic-font-family:auto;
1394 mso-font-pitch:variable;
1395 mso-font-signature:1 0 16778254 0 262144 0;}
1397 {font-family:"Hiragino Sans GB W3";
1398 panose-1:2 11 3 0 0 0 0 0 0 0;
1399 mso-font-charset:80;
1400 mso-generic-font-family:auto;
1401 mso-font-pitch:variable;
1402 mso-font-signature:1 0 16778254 0 262144 0;}
1404 {font-family:"Hiragino Sans GB W6";
1405 panose-1:2 11 6 0 0 0 0 0 0 0;
1406 mso-font-charset:80;
1407 mso-generic-font-family:auto;
1408 mso-font-pitch:variable;
1409 mso-font-signature:1 0 16778254 0 262144 0;}
1412 panose-1:2 0 5 0 0 0 0 0 0 0;
1413 mso-font-charset:80;
1414 mso-generic-font-family:auto;
1415 mso-font-pitch:variable;
1416 mso-font-signature:1 0 16778254 0 262144 0;}
1418 {font-family:\534E\6587\4EFF\5B8B;
1419 mso-font-charset:80;
1420 mso-generic-font-family:auto;
1421 mso-font-pitch:variable;
1422 mso-font-signature:1 0 16778254 0 262144 0;}
1424 {font-family:\534E\6587\9ED1\4F53;
1425 mso-font-charset:80;
1426 mso-generic-font-family:auto;
1427 mso-font-pitch:variable;
1428 mso-font-signature:1 0 16778254 0 262144 0;}
1430 {font-family:\534E\6587\6977\4F53;
1431 mso-font-charset:80;
1432 mso-generic-font-family:auto;
1433 mso-font-pitch:variable;
1434 mso-font-signature:1 0 16778254 0 262144 0;}
1436 {font-family:\534E\6587\5B8B\4F53;
1437 mso-font-charset:80;
1438 mso-generic-font-family:auto;
1439 mso-font-pitch:variable;
1440 mso-font-signature:1 0 16778254 0 262144 0;}
1442 {font-family:\534E\6587\7EC6\9ED1;
1443 mso-font-charset:80;
1444 mso-generic-font-family:auto;
1445 mso-font-pitch:variable;
1446 mso-font-signature:1 0 16778254 0 262144 0;}
1448 {font-family:"MS PGothic";
1449 mso-font-charset:78;
1450 mso-generic-font-family:auto;
1451 mso-font-pitch:variable;
1452 mso-font-signature:1 0 16778247 0 131072 0;}
1454 {font-family:"MS PMincho";
1455 mso-font-charset:78;
1456 mso-generic-font-family:auto;
1457 mso-font-pitch:variable;
1458 mso-font-signature:1 0 16778247 0 131072 0;}
1461 panose-1:2 11 6 0 0 0 0 0 0 0;
1462 mso-font-charset:78;
1463 mso-generic-font-family:auto;
1464 mso-font-pitch:variable;
1465 mso-font-signature:1 0 16778247 0 131072 0;}
1467 {font-family:Osaka\2212\7B49\5E45;
1468 mso-font-charset:78;
1469 mso-generic-font-family:auto;
1470 mso-font-pitch:variable;
1471 mso-font-signature:1 0 16778247 0 131072 0;}
1473 {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
1474 mso-font-charset:78;
1475 mso-generic-font-family:auto;
1476 mso-font-pitch:variable;
1477 mso-font-signature:1 0 16778247 0 131072 0;}
1479 {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W6";
1480 mso-font-charset:78;
1481 mso-generic-font-family:auto;
1482 mso-font-pitch:variable;
1483 mso-font-signature:1 0 16778247 0 131072 0;}
1485 {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 ProN W3";
1486 mso-font-charset:78;
1487 mso-generic-font-family:auto;
1488 mso-font-pitch:variable;
1489 mso-font-signature:1 0 16778247 0 131072 0;}
1491 {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 ProN W6";
1492 mso-font-charset:78;
1493 mso-generic-font-family:auto;
1494 mso-font-pitch:variable;
1495 mso-font-signature:1 0 16778247 0 131072 0;}
1497 {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Std W8";
1498 mso-font-charset:78;
1499 mso-generic-font-family:auto;
1500 mso-font-pitch:variable;
1501 mso-font-signature:1 0 16778247 0 131072 0;}
1503 {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 StdN W8";
1504 mso-font-charset:78;
1505 mso-generic-font-family:auto;
1506 mso-font-pitch:variable;
1507 mso-font-signature:1 0 16778247 0 131072 0;}
1509 {font-family:"\30D2\30E9\30AE\30CE\4E38\30B4 Pro W4";
1510 mso-font-charset:78;
1511 mso-generic-font-family:auto;
1512 mso-font-pitch:variable;
1513 mso-font-signature:1 0 16778247 0 131072 0;}
1515 {font-family:"\30D2\30E9\30AE\30CE\4E38\30B4 ProN W4";
1516 mso-font-charset:78;
1517 mso-generic-font-family:auto;
1518 mso-font-pitch:variable;
1519 mso-font-signature:1 0 16778247 0 131072 0;}
1521 {font-family:"\30D2\30E9\30AE\30CE\660E\671D Pro W3";
1522 mso-font-charset:78;
1523 mso-generic-font-family:auto;
1524 mso-font-pitch:variable;
1525 mso-font-signature:1 0 16778247 0 131072 0;}
1527 {font-family:"\30D2\30E9\30AE\30CE\660E\671D Pro W6";
1528 mso-font-charset:78;
1529 mso-generic-font-family:auto;
1530 mso-font-pitch:variable;
1531 mso-font-signature:1 0 16778247 0 131072 0;}
1533 {font-family:"\30D2\30E9\30AE\30CE\660E\671D ProN W3";
1534 mso-font-charset:78;
1535 mso-generic-font-family:auto;
1536 mso-font-pitch:variable;
1537 mso-font-signature:1 0 16778247 0 131072 0;}
1539 {font-family:"\30D2\30E9\30AE\30CE\660E\671D ProN W6";
1540 mso-font-charset:78;
1541 mso-generic-font-family:auto;
1542 mso-font-pitch:variable;
1543 mso-font-signature:1 0 16778247 0 131072 0;}
1545 {font-family:\30E1\30A4\30EA\30AA;
1546 mso-font-charset:78;
1547 mso-generic-font-family:auto;
1548 mso-font-pitch:variable;
1549 mso-font-signature:1 0 16778247 0 131072 0;}
1551 {font-family:AppleGothic;
1552 panose-1:2 0 5 0 0 0 0 0 0 0;
1553 mso-font-charset:79;
1554 mso-generic-font-family:auto;
1555 mso-font-pitch:variable;
1556 mso-font-signature:1 0 16786438 0 524288 0;}
1558 {font-family:AppleMyungjo;
1559 panose-1:2 0 5 0 0 0 0 0 0 0;
1560 mso-font-charset:79;
1561 mso-generic-font-family:auto;
1562 mso-font-pitch:variable;
1563 mso-font-signature:1 0 16786438 0 524288 0;}
1565 {font-family:PC\BA85\C870;
1566 mso-font-charset:79;
1567 mso-generic-font-family:auto;
1568 mso-font-pitch:variable;
1569 mso-font-signature:1 0 16786438 0 524288 0;}
1571 {font-family:\AD74\B9BC;
1572 mso-font-charset:79;
1573 mso-generic-font-family:auto;
1574 mso-font-pitch:variable;
1575 mso-font-signature:1 0 16786438 0 524288 0;}
1577 {font-family:"FE Modern font face";
1578 mso-font-charset:79;
1579 mso-generic-font-family:auto;
1580 mso-font-pitch:variable;
1581 mso-font-signature:1 0 16786438 0 524288 0;}
1583 {font-family:\D544\AE30\CCB4;
1584 mso-font-charset:79;
1585 mso-generic-font-family:auto;
1586 mso-font-pitch:variable;
1587 mso-font-signature:1 0 16786438 0 524288 0;}
1589 {font-family:\D5E4\B4DC\B77C\C778A;
1590 mso-font-charset:79;
1591 mso-generic-font-family:auto;
1592 mso-font-pitch:variable;
1593 mso-font-signature:1 0 16786438 0 524288 0;}
1595 {font-family:starbats;
1597 mso-generic-font-family:auto;
1598 mso-font-pitch:variable;
1599 mso-font-signature:0 0 0 0 0 0;}
1601 {font-family:Minion-Bold;
1602 panose-1:0 0 0 0 0 0 0 0 0 0;
1603 mso-font-alt:Cambria;
1604 mso-font-charset:77;
1605 mso-generic-font-family:roman;
1606 mso-font-format:other;
1607 mso-font-pitch:auto;
1608 mso-font-signature:3 0 0 0 1 0;}
1610 {font-family:Minion-Regular;
1611 panose-1:0 0 0 0 0 0 0 0 0 0;
1612 mso-font-charset:77;
1613 mso-generic-font-family:roman;
1614 mso-font-format:other;
1615 mso-font-pitch:auto;
1616 mso-font-signature:3 0 0 0 1 0;}
1618 {font-family:Minion-Italic;
1619 panose-1:0 0 0 0 0 0 0 0 0 0;
1620 mso-font-charset:77;
1621 mso-generic-font-family:roman;
1622 mso-font-format:other;
1623 mso-font-pitch:auto;
1624 mso-font-signature:3 0 0 0 1 0;}
1626 {font-family:OfficinaSerif-Bold;
1627 panose-1:0 0 0 0 0 0 0 0 0 0;
1628 mso-font-charset:77;
1629 mso-generic-font-family:roman;
1630 mso-font-format:other;
1631 mso-font-pitch:auto;
1632 mso-font-signature:3 0 0 0 1 0;}
1634 {font-family:Minion-Semibold;
1635 panose-1:0 0 0 0 0 0 0 0 0 0;
1636 mso-font-charset:77;
1637 mso-generic-font-family:roman;
1638 mso-font-format:other;
1639 mso-font-pitch:auto;
1640 mso-font-signature:3 0 0 0 1 0;}
1642 {font-family:OfficinaSans-Book;
1643 panose-1:0 0 0 0 0 0 0 0 0 0;
1644 mso-font-charset:77;
1645 mso-generic-font-family:swiss;
1646 mso-font-format:other;
1647 mso-font-pitch:auto;
1648 mso-font-signature:3 0 0 0 1 0;}
1650 {font-family:OfficinaSans-Bold;
1651 panose-1:0 0 0 0 0 0 0 0 0 0;
1652 mso-font-charset:77;
1653 mso-generic-font-family:swiss;
1654 mso-font-format:other;
1655 mso-font-pitch:auto;
1656 mso-font-signature:3 0 0 0 1 0;}
1658 {font-family:Helvetica-Bold;
1659 panose-1:0 0 0 0 0 0 0 0 0 0;
1660 mso-font-charset:77;
1661 mso-generic-font-family:swiss;
1662 mso-font-format:other;
1663 mso-font-pitch:auto;
1664 mso-font-signature:3 0 0 0 1 0;}
1666 {font-family:OfficinaSerif-Book;
1667 panose-1:0 0 0 0 0 0 0 0 0 0;
1668 mso-font-charset:77;
1669 mso-generic-font-family:roman;
1670 mso-font-format:other;
1671 mso-font-pitch:auto;
1672 mso-font-signature:3 0 0 0 1 0;}
1673 /* Style Definitions */
1674 p.MsoNormal, li.MsoNormal, div.MsoNormal
1675 {mso-style-parent:"";
1677 margin-bottom:.0001pt;
1678 mso-pagination:widow-orphan;
1680 mso-bidi-font-size:10.0pt;
1681 font-family:Garamond;
1682 mso-fareast-font-family:"Times New Roman";
1683 mso-bidi-font-family:"Times New Roman";}
1685 {mso-style-link:"Heading 1 Char";
1686 mso-style-next:"Body Text";
1689 margin-bottom:6.0pt;
1691 mso-pagination:widow-orphan;
1692 page-break-after:avoid;
1693 mso-outline-level:1;
1695 mso-bidi-font-size:10.0pt;
1696 font-family:"Arial Black";
1698 letter-spacing:-1.25pt;
1699 mso-font-kerning:14.0pt;
1700 font-weight:normal;}
1702 {mso-style-update:auto;
1703 mso-style-parent:"Heading 1";
1704 mso-style-next:"Body Text";
1707 margin-bottom:6.0pt;
1709 mso-line-height-alt:12.0pt;
1710 mso-pagination:widow-orphan;
1711 page-break-after:avoid;
1712 mso-outline-level:2;
1714 mso-bidi-font-size:10.0pt;
1715 font-family:"Arial Black";
1717 letter-spacing:-.5pt;
1718 mso-font-kerning:14.0pt;
1719 font-weight:normal;}
1721 {mso-style-update:auto;
1722 mso-style-next:Normal;
1725 margin-bottom:6.0pt;
1728 mso-pagination:none;
1729 page-break-after:avoid;
1730 mso-outline-level:3;
1732 mso-layout-grid-align:none;
1733 punctuation-wrap:simple;
1734 text-autospace:none;
1736 mso-bidi-font-size:10.0pt;
1737 font-family:"Arial Black";
1738 mso-hansi-font-family:Symbol;
1739 font-weight:normal;}
1741 {mso-style-update:auto;
1742 mso-style-parent:MyNormal;
1743 mso-style-next:Normal;
1746 margin-bottom:12.0pt;
1748 mso-pagination:none;
1749 page-break-after:avoid;
1750 mso-outline-level:4;
1752 mso-layout-grid-align:none;
1753 punctuation-wrap:simple;
1754 text-autospace:none;
1756 font-family:"Times New Roman";
1757 mso-bidi-font-family:"Courier New";
1758 text-transform:uppercase;
1759 letter-spacing:1.5pt;
1760 mso-ansi-language:AF;
1761 font-weight:normal;}
1763 {mso-style-next:"Body Text";
1766 margin-bottom:12.0pt;
1768 mso-pagination:widow-orphan;
1769 page-break-after:avoid;
1770 mso-outline-level:5;
1772 mso-element-frame-width:90.0pt;
1773 mso-element-wrap:around;
1774 mso-element-anchor-vertical:paragraph;
1775 mso-element-anchor-horizontal:page;
1776 mso-element-left:60.05pt;
1777 mso-element-top:.05pt;
1778 mso-height-rule:exactly;
1780 mso-bidi-font-size:10.0pt;
1781 font-family:"Arial Black";
1782 letter-spacing:-.25pt;
1783 font-weight:normal;}
1785 {mso-style-next:"Body Text";
1787 margin-bottom:.0001pt;
1788 mso-pagination:widow-orphan;
1789 page-break-after:avoid;
1790 mso-outline-level:6;
1792 mso-element-frame-width:90.0pt;
1793 mso-element-wrap:around;
1794 mso-element-anchor-vertical:paragraph;
1795 mso-element-anchor-horizontal:page;
1796 mso-element-left:60.05pt;
1797 mso-element-top:.05pt;
1798 mso-height-rule:exactly;
1800 mso-bidi-font-size:10.0pt;
1801 font-family:Garamond;
1802 font-weight:normal;}
1803 p.MsoHeading7, li.MsoHeading7, div.MsoHeading7
1804 {mso-style-next:"Body Text";
1809 margin-bottom:.0001pt;
1810 mso-pagination:widow-orphan;
1811 mso-outline-level:7;
1813 mso-shading:windowtext;
1814 mso-pattern:gray-5 auto;
1816 mso-border-alt:solid white .75pt;
1818 mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;
1820 mso-element-frame-width:189.0pt;
1821 mso-element-frame-hspace:12.0pt;
1822 mso-element-wrap:around;
1823 mso-element-anchor-vertical:paragraph;
1824 mso-element-anchor-horizontal:page;
1825 mso-element-left:74.45pt;
1826 mso-element-top:.05pt;
1827 mso-height-rule:exactly;
1829 mso-bidi-font-size:10.0pt;
1830 font-family:Garamond;
1831 mso-fareast-font-family:"Times New Roman";
1832 mso-bidi-font-family:"Times New Roman";
1833 letter-spacing:-.25pt;
1835 mso-bidi-font-style:normal;}
1836 p.MsoHeading8, li.MsoHeading8, div.MsoHeading8
1837 {mso-style-next:"Body Text";
1842 margin-bottom:.0001pt;
1845 mso-line-height-rule:exactly;
1846 mso-pagination:widow-orphan;
1847 page-break-after:avoid;
1848 mso-outline-level:8;
1850 mso-border-top-alt:solid windowtext 3.0pt;
1851 mso-border-bottom-alt:solid windowtext .75pt;
1853 mso-padding-alt:0cm 0cm 0cm 0cm;
1855 mso-element-frame-width:93.0pt;
1856 mso-element-wrap:around;
1857 mso-element-anchor-vertical:paragraph;
1858 mso-element-anchor-horizontal:page;
1859 mso-element-left:60.05pt;
1860 mso-element-top:.05pt;
1861 mso-height-rule:exactly;
1863 mso-bidi-font-size:10.0pt;
1864 font-family:"Arial Black";
1865 mso-fareast-font-family:"Times New Roman";
1866 mso-bidi-font-family:"Times New Roman";
1867 text-transform:uppercase;
1868 letter-spacing:3.0pt;}
1869 p.MsoHeading9, li.MsoHeading9, div.MsoHeading9
1870 {mso-style-next:"Body Text";
1873 margin-bottom:3.0pt;
1875 mso-pagination:widow-orphan;
1876 page-break-after:avoid;
1877 mso-outline-level:9;
1879 mso-bidi-font-size:10.0pt;
1880 font-family:Garamond;
1881 mso-fareast-font-family:"Times New Roman";
1882 mso-bidi-font-family:"Times New Roman";
1883 mso-font-kerning:14.0pt;
1885 mso-bidi-font-weight:normal;
1887 mso-bidi-font-style:normal;}
1888 p.MsoIndex1, li.MsoIndex1, div.MsoIndex1
1889 {mso-style-update:auto;
1890 mso-style-noshow:yes;
1891 mso-style-next:Normal;
1896 margin-bottom:.0001pt;
1898 mso-pagination:widow-orphan;
1900 mso-bidi-font-size:10.0pt;
1901 font-family:Garamond;
1902 mso-fareast-font-family:"Times New Roman";
1903 mso-bidi-font-family:"Times New Roman";}
1904 p.MsoToc1, li.MsoToc1, div.MsoToc1
1905 {mso-style-noshow:yes;
1910 margin-bottom:.0001pt;
1911 mso-pagination:widow-orphan;
1913 font-family:Cambria;
1914 mso-ascii-font-family:Cambria;
1915 mso-ascii-theme-font:minor-latin;
1916 mso-fareast-font-family:"Times New Roman";
1917 mso-hansi-font-family:Cambria;
1918 mso-hansi-theme-font:minor-latin;
1919 mso-bidi-font-family:"Times New Roman";
1921 mso-bidi-font-weight:normal;}
1922 p.MsoToc2, li.MsoToc2, div.MsoToc2
1923 {mso-style-noshow:yes;
1924 mso-style-parent:"TOC 1";
1929 margin-bottom:.0001pt;
1930 mso-pagination:widow-orphan;
1932 font-family:Cambria;
1933 mso-ascii-font-family:Cambria;
1934 mso-ascii-theme-font:minor-latin;
1935 mso-fareast-font-family:"Times New Roman";
1936 mso-hansi-font-family:Cambria;
1937 mso-hansi-theme-font:minor-latin;
1938 mso-bidi-font-family:"Times New Roman";
1940 mso-bidi-font-weight:normal;}
1941 p.MsoToc3, li.MsoToc3, div.MsoToc3
1942 {mso-style-noshow:yes;
1943 mso-style-next:Normal;
1948 margin-bottom:.0001pt;
1949 mso-pagination:widow-orphan;
1951 font-family:Cambria;
1952 mso-ascii-font-family:Cambria;
1953 mso-ascii-theme-font:minor-latin;
1954 mso-fareast-font-family:"Times New Roman";
1955 mso-hansi-font-family:Cambria;
1956 mso-hansi-theme-font:minor-latin;
1957 mso-bidi-font-family:"Times New Roman";}
1958 p.MsoToc4, li.MsoToc4, div.MsoToc4
1959 {mso-style-noshow:yes;
1960 mso-style-next:Normal;
1965 margin-bottom:.0001pt;
1966 mso-pagination:widow-orphan;
1968 font-family:Cambria;
1969 mso-ascii-font-family:Cambria;
1970 mso-ascii-theme-font:minor-latin;
1971 mso-fareast-font-family:"Times New Roman";
1972 mso-hansi-font-family:Cambria;
1973 mso-hansi-theme-font:minor-latin;
1974 mso-bidi-font-family:"Times New Roman";}
1975 p.MsoToc5, li.MsoToc5, div.MsoToc5
1976 {mso-style-update:auto;
1977 mso-style-noshow:yes;
1978 mso-style-next:Normal;
1983 margin-bottom:.0001pt;
1984 mso-pagination:widow-orphan;
1986 font-family:Cambria;
1987 mso-ascii-font-family:Cambria;
1988 mso-ascii-theme-font:minor-latin;
1989 mso-fareast-font-family:"Times New Roman";
1990 mso-hansi-font-family:Cambria;
1991 mso-hansi-theme-font:minor-latin;
1992 mso-bidi-font-family:"Times New Roman";}
1993 p.MsoToc6, li.MsoToc6, div.MsoToc6
1994 {mso-style-update:auto;
1995 mso-style-noshow:yes;
1996 mso-style-next:Normal;
2001 margin-bottom:.0001pt;
2002 mso-pagination:widow-orphan;
2004 font-family:Cambria;
2005 mso-ascii-font-family:Cambria;
2006 mso-ascii-theme-font:minor-latin;
2007 mso-fareast-font-family:"Times New Roman";
2008 mso-hansi-font-family:Cambria;
2009 mso-hansi-theme-font:minor-latin;
2010 mso-bidi-font-family:"Times New Roman";}
2011 p.MsoToc7, li.MsoToc7, div.MsoToc7
2012 {mso-style-update:auto;
2013 mso-style-noshow:yes;
2014 mso-style-next:Normal;
2019 margin-bottom:.0001pt;
2020 mso-pagination:widow-orphan;
2022 font-family:Cambria;
2023 mso-ascii-font-family:Cambria;
2024 mso-ascii-theme-font:minor-latin;
2025 mso-fareast-font-family:"Times New Roman";
2026 mso-hansi-font-family:Cambria;
2027 mso-hansi-theme-font:minor-latin;
2028 mso-bidi-font-family:"Times New Roman";}
2029 p.MsoToc8, li.MsoToc8, div.MsoToc8
2030 {mso-style-update:auto;
2031 mso-style-noshow:yes;
2032 mso-style-next:Normal;
2037 margin-bottom:.0001pt;
2038 mso-pagination:widow-orphan;
2040 font-family:Cambria;
2041 mso-ascii-font-family:Cambria;
2042 mso-ascii-theme-font:minor-latin;
2043 mso-fareast-font-family:"Times New Roman";
2044 mso-hansi-font-family:Cambria;
2045 mso-hansi-theme-font:minor-latin;
2046 mso-bidi-font-family:"Times New Roman";}
2047 p.MsoToc9, li.MsoToc9, div.MsoToc9
2048 {mso-style-update:auto;
2049 mso-style-noshow:yes;
2050 mso-style-next:Normal;
2055 margin-bottom:.0001pt;
2056 mso-pagination:widow-orphan;
2058 font-family:Cambria;
2059 mso-ascii-font-family:Cambria;
2060 mso-ascii-theme-font:minor-latin;
2061 mso-fareast-font-family:"Times New Roman";
2062 mso-hansi-font-family:Cambria;
2063 mso-hansi-theme-font:minor-latin;
2064 mso-bidi-font-family:"Times New Roman";}
2065 p.MsoHeader, li.MsoHeader, div.MsoHeader
2067 margin-bottom:.0001pt;
2068 mso-pagination:widow-orphan lines-together;
2069 tab-stops:center 216.0pt right 432.0pt;
2071 mso-bidi-font-size:10.0pt;
2072 font-family:"Arial Black";
2073 mso-fareast-font-family:"Times New Roman";
2074 mso-bidi-font-family:"Times New Roman";
2075 text-transform:uppercase;
2076 letter-spacing:3.0pt;}
2077 p.MsoFooter, li.MsoFooter, div.MsoFooter
2079 margin-bottom:.0001pt;
2081 mso-pagination:widow-orphan lines-together;
2082 tab-stops:center 216.0pt right 432.0pt;
2084 mso-border-top-alt:solid windowtext .75pt;
2086 mso-padding-alt:3.0pt 0cm 0cm 0cm;
2088 mso-bidi-font-size:10.0pt;
2089 font-family:"Arial Black";
2090 mso-fareast-font-family:"Times New Roman";
2091 mso-bidi-font-family:"Times New Roman";}
2092 p.MsoCaption, li.MsoCaption, div.MsoCaption
2093 {mso-style-next:"Body Text";
2096 margin-bottom:12.0pt;
2098 mso-pagination:widow-orphan;
2100 mso-bidi-font-size:10.0pt;
2101 font-family:Garamond;
2102 mso-fareast-font-family:"Times New Roman";
2103 mso-bidi-font-family:"Times New Roman";
2104 letter-spacing:-.25pt;}
2105 span.MsoCommentReference
2106 {mso-style-noshow:yes;
2107 mso-style-parent:"";
2108 mso-ansi-font-size:8.0pt;}
2110 {mso-style-parent:"";
2111 mso-ansi-font-size:9.0pt;
2113 mso-ascii-font-family:Arial;
2114 mso-hansi-font-family:Arial;
2115 mso-bidi-font-family:Arial;}
2117 {mso-style-parent:"";
2119 mso-bidi-font-weight:normal;}
2120 p.MsoList, li.MsoList, div.MsoList
2121 {mso-style-parent:"Body Text";
2122 mso-style-link:"List Char";
2125 margin-bottom:12.0pt;
2128 mso-pagination:widow-orphan;
2131 mso-bidi-font-size:10.0pt;
2132 font-family:Garamond;
2133 mso-fareast-font-family:"Times New Roman";
2134 mso-bidi-font-family:"Times New Roman";
2135 letter-spacing:-.25pt;}
2136 p.MsoListBullet, li.MsoListBullet, div.MsoListBullet
2137 {mso-style-parent:List;
2140 margin-bottom:12.0pt;
2144 mso-pagination:widow-orphan;
2145 mso-list:l25 level1 lfo5;
2147 mso-bidi-font-size:10.0pt;
2148 font-family:Garamond;
2149 mso-fareast-font-family:"Times New Roman";
2150 mso-bidi-font-family:"Times New Roman";
2151 letter-spacing:-.25pt;}
2152 p.MsoListNumber, li.MsoListNumber, div.MsoListNumber
2153 {mso-style-parent:List;
2155 margin-right:18.0pt;
2156 margin-bottom:12.0pt;
2159 text-indent:-18.0pt;
2160 mso-pagination:widow-orphan;
2161 mso-list:l8 level1 lfo7;
2163 mso-bidi-font-size:10.0pt;
2164 font-family:Garamond;
2165 mso-fareast-font-family:"Times New Roman";
2166 mso-bidi-font-family:"Times New Roman";
2167 letter-spacing:-.25pt;}
2168 p.MsoList2, li.MsoList2, div.MsoList2
2169 {mso-style-parent:List;
2172 margin-bottom:12.0pt;
2175 mso-pagination:widow-orphan;
2178 mso-bidi-font-size:10.0pt;
2179 font-family:Garamond;
2180 mso-fareast-font-family:"Times New Roman";
2181 mso-bidi-font-family:"Times New Roman";
2182 letter-spacing:-.25pt;}
2183 p.MsoList3, li.MsoList3, div.MsoList3
2184 {mso-style-parent:List;
2187 margin-bottom:12.0pt;
2190 mso-pagination:widow-orphan;
2193 mso-bidi-font-size:10.0pt;
2194 font-family:Garamond;
2195 mso-fareast-font-family:"Times New Roman";
2196 mso-bidi-font-family:"Times New Roman";
2197 letter-spacing:-.25pt;}
2198 p.MsoList4, li.MsoList4, div.MsoList4
2199 {mso-style-parent:List;
2202 margin-bottom:12.0pt;
2205 mso-pagination:widow-orphan;
2208 mso-bidi-font-size:10.0pt;
2209 font-family:Garamond;
2210 mso-fareast-font-family:"Times New Roman";
2211 mso-bidi-font-family:"Times New Roman";
2212 letter-spacing:-.25pt;}
2213 p.MsoList5, li.MsoList5, div.MsoList5
2214 {mso-style-parent:List;
2217 margin-bottom:12.0pt;
2218 margin-left:108.0pt;
2220 mso-pagination:widow-orphan;
2223 mso-bidi-font-size:10.0pt;
2224 font-family:Garamond;
2225 mso-fareast-font-family:"Times New Roman";
2226 mso-bidi-font-family:"Times New Roman";
2227 letter-spacing:-.25pt;}
2228 p.MsoListBullet2, li.MsoListBullet2, div.MsoListBullet2
2229 {mso-style-parent:"List Bullet";
2232 margin-bottom:12.0pt;
2236 mso-pagination:widow-orphan;
2237 mso-list:l7 level1 lfo8;
2239 mso-bidi-font-size:10.0pt;
2240 font-family:Garamond;
2241 mso-fareast-font-family:"Times New Roman";
2242 mso-bidi-font-family:"Times New Roman";
2243 letter-spacing:-.25pt;}
2244 p.MsoListBullet3, li.MsoListBullet3, div.MsoListBullet3
2245 {mso-style-parent:"List Bullet";
2248 margin-bottom:12.0pt;
2252 mso-pagination:widow-orphan;
2253 mso-list:l6 level1 lfo9;
2255 mso-bidi-font-size:10.0pt;
2256 font-family:Garamond;
2257 mso-fareast-font-family:"Times New Roman";
2258 mso-bidi-font-family:"Times New Roman";
2259 letter-spacing:-.25pt;}
2260 p.MsoListBullet4, li.MsoListBullet4, div.MsoListBullet4
2261 {mso-style-parent:"List Bullet";
2264 margin-bottom:12.0pt;
2268 mso-pagination:widow-orphan;
2269 mso-list:l5 level1 lfo10;
2271 mso-bidi-font-size:10.0pt;
2272 font-family:Garamond;
2273 mso-fareast-font-family:"Times New Roman";
2274 mso-bidi-font-family:"Times New Roman";
2275 letter-spacing:-.25pt;}
2276 p.MsoListBullet5, li.MsoListBullet5, div.MsoListBullet5
2278 margin-right:18.0pt;
2281 margin-bottom:.0001pt;
2282 text-indent:-18.0pt;
2284 mso-line-height-rule:exactly;
2285 mso-pagination:widow-orphan;
2286 mso-list:l22 level1 lfo12;
2287 tab-stops:list 18.0pt;
2289 mso-border-bottom-alt:solid windowtext .75pt;
2291 mso-padding-alt:0cm 0cm 0cm 0cm;
2293 mso-element-frame-width:93.0pt;
2294 mso-element-wrap:around;
2295 mso-element-anchor-vertical:paragraph;
2296 mso-element-anchor-horizontal:page;
2297 mso-element-left:60.05pt;
2298 mso-element-top:.05pt;
2299 mso-height-rule:exactly;
2301 mso-bidi-font-size:10.0pt;
2302 font-family:Garamond;
2303 mso-fareast-font-family:"Times New Roman";
2304 mso-bidi-font-family:"Times New Roman";}
2305 p.MsoListNumber2, li.MsoListNumber2, div.MsoListNumber2
2306 {mso-style-parent:"List Number";
2308 margin-right:18.0pt;
2309 margin-bottom:12.0pt;
2312 text-indent:-18.0pt;
2313 mso-pagination:widow-orphan;
2314 mso-list:l3 level1 lfo14;
2316 mso-bidi-font-size:10.0pt;
2317 font-family:Garamond;
2318 mso-fareast-font-family:"Times New Roman";
2319 mso-bidi-font-family:"Times New Roman";
2320 letter-spacing:-.25pt;}
2321 p.MsoListNumber3, li.MsoListNumber3, div.MsoListNumber3
2322 {mso-style-parent:"List Number";
2324 margin-right:18.0pt;
2325 margin-bottom:12.0pt;
2328 text-indent:-18.0pt;
2329 mso-pagination:widow-orphan;
2330 mso-list:l2 level1 lfo15;
2332 mso-bidi-font-size:10.0pt;
2333 font-family:Garamond;
2334 mso-fareast-font-family:"Times New Roman";
2335 mso-bidi-font-family:"Times New Roman";
2336 letter-spacing:-.25pt;}
2337 p.MsoListNumber4, li.MsoListNumber4, div.MsoListNumber4
2338 {mso-style-parent:"List Number";
2340 margin-right:18.0pt;
2341 margin-bottom:12.0pt;
2344 text-indent:-18.0pt;
2345 mso-pagination:widow-orphan;
2346 mso-list:l1 level1 lfo16;
2348 mso-bidi-font-size:10.0pt;
2349 font-family:Garamond;
2350 mso-fareast-font-family:"Times New Roman";
2351 mso-bidi-font-family:"Times New Roman";
2352 letter-spacing:-.25pt;}
2353 p.MsoListNumber5, li.MsoListNumber5, div.MsoListNumber5
2354 {mso-style-parent:"List Number";
2356 margin-right:18.0pt;
2357 margin-bottom:12.0pt;
2358 margin-left:108.0pt;
2360 text-indent:-18.0pt;
2361 mso-pagination:widow-orphan;
2362 mso-list:l0 level1 lfo17;
2364 mso-bidi-font-size:10.0pt;
2365 font-family:Garamond;
2366 mso-fareast-font-family:"Times New Roman";
2367 mso-bidi-font-family:"Times New Roman";
2368 letter-spacing:-.25pt;}
2369 p.MsoTitle, li.MsoTitle, div.MsoTitle
2370 {mso-style-parent:"Heading Base";
2373 margin-bottom:180.0pt;
2377 mso-line-height-rule:exactly;
2378 mso-pagination:widow-orphan;
2379 page-break-after:avoid;
2381 mso-border-bottom-alt:solid gray .75pt;
2383 mso-padding-alt:0cm 0cm 14.0pt 0cm;
2385 mso-bidi-font-size:10.0pt;
2386 font-family:"Arial Black";
2387 mso-fareast-font-family:"Times New Roman";
2388 mso-bidi-font-family:"Times New Roman";
2390 letter-spacing:-1.75pt;
2391 mso-font-kerning:14.0pt;}
2392 p.MsoBodyText, li.MsoBodyText, div.MsoBodyText
2395 margin-bottom:12.0pt;
2398 mso-pagination:widow-orphan;
2400 mso-bidi-font-size:10.0pt;
2401 font-family:Garamond;
2402 mso-fareast-font-family:"Times New Roman";
2403 mso-bidi-font-family:"Times New Roman";
2404 letter-spacing:-.25pt;}
2405 p.MsoBodyTextIndent, li.MsoBodyTextIndent, div.MsoBodyTextIndent
2406 {mso-style-parent:"Body Text";
2409 margin-bottom:12.0pt;
2413 mso-pagination:widow-orphan;
2415 mso-bidi-font-size:10.0pt;
2416 font-family:Garamond;
2417 mso-fareast-font-family:"Times New Roman";
2418 mso-bidi-font-family:"Times New Roman";
2419 letter-spacing:-.25pt;}
2420 p.MsoListContinue, li.MsoListContinue, div.MsoListContinue
2421 {mso-style-parent:List;
2424 margin-bottom:8.0pt;
2427 mso-pagination:widow-orphan;
2429 mso-bidi-font-size:10.0pt;
2430 font-family:Garamond;
2431 mso-fareast-font-family:"Times New Roman";
2432 mso-bidi-font-family:"Times New Roman";
2433 letter-spacing:-.25pt;}
2434 p.MsoListContinue2, li.MsoListContinue2, div.MsoListContinue2
2435 {mso-style-parent:"List Continue";
2438 margin-bottom:8.0pt;
2441 mso-pagination:widow-orphan;
2443 mso-bidi-font-size:10.0pt;
2444 font-family:Garamond;
2445 mso-fareast-font-family:"Times New Roman";
2446 mso-bidi-font-family:"Times New Roman";
2447 letter-spacing:-.25pt;}
2448 p.MsoListContinue3, li.MsoListContinue3, div.MsoListContinue3
2449 {mso-style-parent:"List Continue";
2452 margin-bottom:8.0pt;
2455 mso-pagination:widow-orphan;
2457 mso-bidi-font-size:10.0pt;
2458 font-family:Garamond;
2459 mso-fareast-font-family:"Times New Roman";
2460 mso-bidi-font-family:"Times New Roman";
2461 letter-spacing:-.25pt;}
2462 p.MsoListContinue4, li.MsoListContinue4, div.MsoListContinue4
2463 {mso-style-parent:"List Continue";
2466 margin-bottom:8.0pt;
2469 mso-pagination:widow-orphan;
2471 mso-bidi-font-size:10.0pt;
2472 font-family:Garamond;
2473 mso-fareast-font-family:"Times New Roman";
2474 mso-bidi-font-family:"Times New Roman";
2475 letter-spacing:-.25pt;}
2476 p.MsoListContinue5, li.MsoListContinue5, div.MsoListContinue5
2477 {mso-style-parent:"List Continue";
2480 margin-bottom:8.0pt;
2481 margin-left:108.0pt;
2483 mso-pagination:widow-orphan;
2485 mso-bidi-font-size:10.0pt;
2486 font-family:Garamond;
2487 mso-fareast-font-family:"Times New Roman";
2488 mso-bidi-font-family:"Times New Roman";
2489 letter-spacing:-.25pt;}
2490 p.MsoSubtitle, li.MsoSubtitle, div.MsoSubtitle
2491 {mso-style-parent:Title;
2492 mso-style-next:"Body Text";
2497 margin-bottom:.0001pt;
2500 mso-pagination:widow-orphan;
2501 page-break-after:avoid;
2503 mso-border-bottom-alt:solid gray .75pt;
2505 mso-padding-alt:0cm 0cm 14.0pt 0cm;
2507 mso-bidi-font-size:10.0pt;
2508 font-family:Garamond;
2509 mso-fareast-font-family:"Times New Roman";
2510 mso-bidi-font-family:"Times New Roman";
2512 text-transform:uppercase;
2513 letter-spacing:1.5pt;
2514 mso-font-kerning:14.0pt;
2515 mso-bidi-font-weight:bold;}
2516 p.MsoDate, li.MsoDate, div.MsoDate
2517 {mso-style-parent:"Body Text";
2520 margin-bottom:8.0pt;
2523 mso-pagination:widow-orphan;
2525 font-family:"Times New Roman";
2526 mso-fareast-font-family:"Times New Roman";
2527 mso-bidi-font-family:"Times New Roman";
2529 mso-bidi-font-weight:normal;}
2530 a:link, span.MsoHyperlink
2532 text-decoration:underline;
2533 text-underline:single;}
2534 a:visited, span.MsoHyperlinkFollowed
2536 text-decoration:underline;
2537 text-underline:single;}
2539 {mso-style-parent:"";
2540 mso-ansi-font-size:9.0pt;
2541 font-family:"Arial Black";
2542 mso-ascii-font-family:"Arial Black";
2543 mso-hansi-font-family:"Arial Black";
2545 p.MsoPlainText, li.MsoPlainText, div.MsoPlainText
2547 margin-bottom:.0001pt;
2548 mso-pagination:widow-orphan;
2550 font-family:"Courier New";
2551 mso-fareast-font-family:"Times New Roman";
2552 mso-bidi-font-family:"Courier New";
2553 mso-ansi-language:FR;
2554 mso-fareast-language:FR;}
2556 {mso-bidi-font-size:10.0pt;
2557 font-family:"Courier New";
2558 mso-ascii-font-family:"Courier New";
2559 mso-fareast-font-family:"MS Mincho";
2560 mso-hansi-font-family:"Courier New";
2561 mso-bidi-font-family:"Courier New";}
2563 {mso-style-name:"Heading 1 Char";
2564 mso-style-locked:yes;
2565 mso-style-link:"Heading 1";
2566 mso-ansi-font-size:16.0pt;
2567 font-family:"Arial Black";
2568 mso-ascii-font-family:"Arial Black";
2569 mso-hansi-font-family:"Arial Black";
2571 letter-spacing:-1.25pt;
2572 mso-font-kerning:14.0pt;
2573 mso-ansi-language:EN-US;
2574 mso-fareast-language:EN-US;}
2575 p.MyNormal, li.MyNormal, div.MyNormal
2576 {mso-style-name:MyNormal;
2577 mso-style-update:auto;
2578 mso-style-link:"MyNormal Char";
2581 margin-bottom:6.0pt;
2582 margin-left:42.55pt;
2584 mso-pagination:none;
2586 mso-layout-grid-align:none;
2587 punctuation-wrap:simple;
2588 text-autospace:none;
2590 font-family:"Times New Roman";
2591 mso-fareast-font-family:"Times New Roman";
2592 mso-bidi-font-family:"Courier New";
2593 mso-ansi-language:AF;}
2595 {mso-style-name:"MyNormal Char";
2596 mso-style-locked:yes;
2597 mso-style-parent:"example Char";
2598 mso-style-link:MyNormal;
2599 mso-ansi-font-size:11.0pt;
2600 mso-bidi-font-size:11.0pt;
2601 font-family:"Courier New";
2602 mso-ascii-font-family:"Courier New";
2603 mso-hansi-font-family:"Courier New";
2604 mso-bidi-font-family:"Courier New";
2605 mso-ansi-language:AF;
2606 mso-fareast-language:EN-US;}
2608 {mso-style-name:"example Char";
2609 mso-style-locked:yes;
2610 mso-style-link:example;
2611 mso-ansi-font-size:8.0pt;
2612 font-family:"Courier New";
2613 mso-ascii-font-family:"Courier New";
2614 mso-hansi-font-family:"Courier New";
2615 mso-bidi-font-family:"Courier New";
2616 mso-ansi-language:EN-US;
2617 mso-fareast-language:EN-US;}
2618 p.example, li.example, div.example
2619 {mso-style-name:example;
2620 mso-style-update:auto;
2621 mso-style-link:"example Char";
2624 margin-bottom:6.0pt;
2627 mso-pagination:none;
2629 mso-layout-grid-align:none;
2630 punctuation-wrap:simple;
2631 text-autospace:none;
2633 mso-bidi-font-size:10.0pt;
2634 font-family:"Courier New";
2635 mso-fareast-font-family:"Times New Roman";
2636 mso-bidi-font-family:"Courier New";}
2637 p.FAQ, li.FAQ, div.FAQ
2638 {mso-style-name:FAQ;
2639 mso-style-update:auto;
2640 mso-style-parent:MyNormal;
2643 margin-bottom:6.0pt;
2646 mso-pagination:none;
2648 mso-layout-grid-align:none;
2649 punctuation-wrap:simple;
2650 text-autospace:none;
2652 mso-bidi-font-size:14.0pt;
2653 font-family:"Comic Sans MS";
2654 mso-fareast-font-family:"Times New Roman";
2655 mso-bidi-font-family:"Courier New";
2656 mso-ansi-language:EN-GB;
2658 mso-bidi-font-weight:normal;}
2660 {mso-style-name:"List Char";
2661 mso-style-locked:yes;
2662 mso-style-parent:"Text body Char";
2663 mso-style-link:List;
2664 mso-ansi-font-size:12.0pt;
2665 font-family:Garamond;
2666 mso-ascii-font-family:Garamond;
2667 mso-hansi-font-family:Garamond;
2668 letter-spacing:-.25pt;
2669 mso-ansi-language:EN-US;
2670 mso-fareast-language:EN-US;}
2672 {mso-style-name:"Text body Char";
2673 mso-style-locked:yes;
2674 mso-style-link:"Text body";
2675 mso-ansi-font-size:12.0pt;
2676 mso-ansi-language:EN-US;
2677 mso-fareast-language:EN-US;}
2678 p.Textbody, li.Textbody, div.Textbody
2679 {mso-style-name:"Text body";
2680 mso-style-link:"Text body Char";
2682 margin-bottom:.0001pt;
2684 mso-pagination:none;
2686 mso-layout-grid-align:none;
2687 punctuation-wrap:simple;
2688 text-autospace:none;
2690 mso-bidi-font-size:10.0pt;
2691 font-family:"Times New Roman";
2692 mso-fareast-font-family:"Times New Roman";
2693 mso-bidi-font-family:"Times New Roman";}
2694 p.HeadingBase, li.HeadingBase, div.HeadingBase
2695 {mso-style-name:"Heading Base";
2696 mso-style-next:"Body Text";
2699 margin-bottom:6.0pt;
2701 mso-pagination:widow-orphan;
2702 page-break-after:avoid;
2704 mso-bidi-font-size:10.0pt;
2706 mso-fareast-font-family:"Times New Roman";
2707 mso-bidi-font-family:"Times New Roman";
2708 mso-font-kerning:14.0pt;
2710 mso-bidi-font-weight:normal;}
2711 p.BlockQuotation, li.BlockQuotation, div.BlockQuotation
2712 {mso-style-name:"Block Quotation";
2713 mso-style-next:"Body Text";
2715 margin-right:30.0pt;
2716 margin-bottom:12.0pt;
2719 mso-pagination:widow-orphan;
2721 mso-shading:windowtext;
2722 mso-pattern:gray-10 gray;
2724 mso-border-alt:solid white .75pt;
2726 mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;
2728 mso-bidi-font-size:10.0pt;
2729 font-family:Garamond;
2730 mso-fareast-font-family:"Times New Roman";
2731 mso-bidi-font-family:"Times New Roman";
2732 letter-spacing:-.25pt;}
2733 p.BlockQuotationFirst, li.BlockQuotationFirst, div.BlockQuotationFirst
2734 {mso-style-name:"Block Quotation First";
2735 mso-style-next:"Block Quotation";
2737 margin-right:24.0pt;
2740 margin-bottom:.0001pt;
2742 mso-pagination:widow-orphan lines-together;
2744 mso-shading:windowtext;
2745 mso-pattern:gray-10 auto;
2747 mso-border-top-alt:solid white .75pt;
2748 mso-border-left-alt:solid white .75pt;
2749 mso-border-right-alt:solid white .75pt;
2751 mso-padding-alt:6.0pt 6.0pt 0cm 6.0pt;
2753 mso-bidi-font-size:10.0pt;
2754 font-family:"Arial Black";
2755 mso-fareast-font-family:"Times New Roman";
2756 mso-bidi-font-family:"Times New Roman";
2757 letter-spacing:-.5pt;}
2758 p.BlockQuotationLast, li.BlockQuotationLast, div.BlockQuotationLast
2759 {mso-style-name:"Block Quotation Last";
2760 mso-style-parent:"Block Quotation";
2761 mso-style-next:"Body Text";
2763 margin-right:36.0pt;
2764 margin-bottom:12.0pt;
2766 mso-pagination:widow-orphan lines-together;
2768 font-family:"Times New Roman";
2769 mso-fareast-font-family:"Times New Roman";
2770 mso-bidi-font-family:"Times New Roman";
2772 mso-bidi-font-style:normal;}
2773 p.BodyTextKeep, li.BodyTextKeep, div.BodyTextKeep
2774 {mso-style-name:"Body Text Keep";
2775 mso-style-parent:"Body Text";
2776 mso-style-next:"Body Text";
2779 margin-bottom:12.0pt;
2782 mso-pagination:widow-orphan;
2783 page-break-after:avoid;
2785 mso-bidi-font-size:10.0pt;
2786 font-family:Garamond;
2787 mso-fareast-font-family:"Times New Roman";
2788 mso-bidi-font-family:"Times New Roman";
2789 letter-spacing:-.25pt;}
2790 p.ChapterLabel, li.ChapterLabel, div.ChapterLabel
2791 {mso-style-name:"Chapter Label";
2792 mso-style-next:"Body Text";
2795 margin-bottom:12.0pt;
2797 mso-pagination:widow-orphan;
2798 page-break-after:avoid;
2800 mso-border-bottom-alt:solid windowtext .75pt;
2802 mso-padding-alt:0cm 0cm 3.0pt 0cm;
2804 mso-bidi-font-size:10.0pt;
2805 font-family:"Arial Black";
2806 mso-fareast-font-family:"Times New Roman";
2807 mso-bidi-font-family:"Times New Roman";
2808 text-transform:uppercase;
2809 letter-spacing:3.5pt;
2810 mso-font-kerning:14.0pt;}
2811 p.ChapterSubtitle, li.ChapterSubtitle, div.ChapterSubtitle
2812 {mso-style-name:"Chapter Subtitle";
2813 mso-style-next:"Body Text";
2815 margin-right:90.0pt;
2816 margin-bottom:18.0pt;
2818 mso-line-height-alt:12.0pt;
2819 mso-pagination:widow-orphan lines-together;
2820 page-break-after:avoid;
2822 mso-bidi-font-size:10.0pt;
2823 font-family:Garamond;
2824 mso-fareast-font-family:"Times New Roman";
2825 mso-bidi-font-family:"Times New Roman";
2826 letter-spacing:-1.0pt;
2827 mso-font-kerning:14.0pt;
2829 mso-bidi-font-style:normal;}
2830 p.ChapterTitle, li.ChapterTitle, div.ChapterTitle
2831 {mso-style-name:"Chapter Title";
2832 mso-style-update:auto;
2833 mso-style-link:"Chapter Title Char";
2834 mso-style-next:"Chapter Subtitle";
2836 margin-right:4.25pt;
2837 margin-bottom:102.0pt;
2840 mso-line-height-alt:22.0pt;
2841 page-break-before:always;
2842 mso-pagination:widow-orphan lines-together;
2843 page-break-after:avoid;
2846 mso-border-alt:solid windowtext 3.0pt;
2848 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
2850 mso-bidi-font-size:48.0pt;
2851 font-family:"Arial Black";
2852 mso-fareast-font-family:"Times New Roman";
2853 mso-bidi-font-family:"Times New Roman";
2855 letter-spacing:-1.75pt;
2856 mso-font-kerning:14.0pt;}
2857 span.ChapterTitleChar
2858 {mso-style-name:"Chapter Title Char";
2859 mso-style-locked:yes;
2860 mso-style-link:"Chapter Title";
2861 mso-ansi-font-size:36.0pt;
2862 mso-bidi-font-size:48.0pt;
2863 font-family:"Arial Black";
2864 mso-ascii-font-family:"Arial Black";
2865 mso-hansi-font-family:"Arial Black";
2867 letter-spacing:-1.75pt;
2868 mso-font-kerning:14.0pt;
2869 mso-ansi-language:EN-US;
2870 mso-fareast-language:EN-US;}
2871 p.CompanyName, li.CompanyName, div.CompanyName
2872 {mso-style-name:"Company Name";
2873 mso-style-next:Normal;
2876 margin-bottom:3.0pt;
2879 mso-line-height-rule:exactly;
2880 mso-pagination:widow-orphan;
2882 mso-bidi-font-size:10.0pt;
2883 font-family:Garamond;
2884 mso-fareast-font-family:"Times New Roman";
2885 mso-bidi-font-family:"Times New Roman";
2886 text-transform:uppercase;
2887 mso-font-kerning:18.0pt;}
2888 p.DocumentLabel, li.DocumentLabel, div.DocumentLabel
2889 {mso-style-name:"Document Label";
2892 margin-bottom:18.0pt;
2894 mso-pagination:widow-orphan;
2895 page-break-after:avoid;
2897 mso-bidi-font-size:10.0pt;
2898 font-family:Garamond;
2899 mso-fareast-font-family:"Times New Roman";
2900 mso-bidi-font-family:"Times New Roman";
2901 mso-font-kerning:14.0pt;
2903 mso-bidi-font-weight:normal;}
2904 p.FooterEven, li.FooterEven, div.FooterEven
2905 {mso-style-name:"Footer Even";
2906 mso-style-parent:Footer;
2908 margin-bottom:.0001pt;
2910 mso-pagination:widow-orphan lines-together;
2911 tab-stops:center 216.0pt right 432.0pt;
2913 mso-border-top-alt:solid windowtext .75pt;
2915 mso-padding-alt:3.0pt 0cm 0cm 0cm;
2917 mso-bidi-font-size:10.0pt;
2918 font-family:"Arial Black";
2919 mso-fareast-font-family:"Times New Roman";
2920 mso-bidi-font-family:"Times New Roman";}
2921 p.FooterFirst, li.FooterFirst, div.FooterFirst
2922 {mso-style-name:"Footer First";
2923 mso-style-parent:Footer;
2925 margin-bottom:.0001pt;
2927 mso-pagination:widow-orphan lines-together;
2928 tab-stops:center 216.0pt;
2930 mso-bidi-font-size:10.0pt;
2931 font-family:"Arial Black";
2932 mso-fareast-font-family:"Times New Roman";
2933 mso-bidi-font-family:"Times New Roman";
2934 letter-spacing:-.5pt;}
2935 p.FooterOdd, li.FooterOdd, div.FooterOdd
2936 {mso-style-name:"Footer Odd";
2937 mso-style-parent:Footer;
2939 margin-bottom:.0001pt;
2941 mso-pagination:widow-orphan lines-together;
2942 tab-stops:right 0cm center 216.0pt right 432.0pt;
2944 mso-border-top-alt:solid windowtext .75pt;
2946 mso-padding-alt:3.0pt 0cm 0cm 0cm;
2948 mso-bidi-font-size:10.0pt;
2949 font-family:"Arial Black";
2950 mso-fareast-font-family:"Times New Roman";
2951 mso-bidi-font-family:"Times New Roman";}
2952 p.FootnoteBase, li.FootnoteBase, div.FootnoteBase
2953 {mso-style-name:"Footnote Base";
2958 margin-bottom:.0001pt;
2959 mso-pagination:widow-orphan;
2961 mso-bidi-font-size:10.0pt;
2962 font-family:Garamond;
2963 mso-fareast-font-family:"Times New Roman";
2964 mso-bidi-font-family:"Times New Roman";}
2965 p.HeaderBase, li.HeaderBase, div.HeaderBase
2966 {mso-style-name:"Header Base";
2968 margin-bottom:.0001pt;
2969 mso-pagination:widow-orphan lines-together;
2970 tab-stops:center 216.0pt right 432.0pt;
2972 mso-bidi-font-size:10.0pt;
2973 font-family:Garamond;
2974 mso-fareast-font-family:"Times New Roman";
2975 mso-bidi-font-family:"Times New Roman";}
2976 p.HeaderEven, li.HeaderEven, div.HeaderEven
2977 {mso-style-name:"Header Even";
2978 mso-style-parent:Header;
2980 margin-bottom:.0001pt;
2981 mso-pagination:widow-orphan lines-together;
2982 tab-stops:center 216.0pt right 432.0pt;
2984 mso-bidi-font-size:10.0pt;
2985 font-family:"Arial Black";
2986 mso-fareast-font-family:"Times New Roman";
2987 mso-bidi-font-family:"Times New Roman";
2988 text-transform:uppercase;
2989 letter-spacing:3.0pt;}
2990 p.HeaderFirst, li.HeaderFirst, div.HeaderFirst
2991 {mso-style-name:"Header First";
2992 mso-style-parent:Header;
2994 margin-bottom:.0001pt;
2995 mso-pagination:widow-orphan lines-together;
2996 tab-stops:center 216.0pt;
2998 mso-bidi-font-size:10.0pt;
2999 font-family:Garamond;
3000 mso-fareast-font-family:"Times New Roman";
3001 mso-bidi-font-family:"Times New Roman";
3002 text-transform:uppercase;
3003 letter-spacing:3.0pt;
3005 mso-bidi-font-weight:normal;}
3006 p.HeaderOdd, li.HeaderOdd, div.HeaderOdd
3007 {mso-style-name:"Header Odd";
3008 mso-style-parent:Header;
3010 margin-bottom:.0001pt;
3012 mso-pagination:widow-orphan lines-together;
3013 tab-stops:right 0cm center 216.0pt right 432.0pt;
3015 mso-bidi-font-size:10.0pt;
3016 font-family:"Arial Black";
3017 mso-fareast-font-family:"Times New Roman";
3018 mso-bidi-font-family:"Times New Roman";
3019 text-transform:uppercase;
3020 letter-spacing:3.0pt;}
3021 p.Icon1, li.Icon1, div.Icon1
3022 {mso-style-name:"Icon 1";
3027 margin-bottom:.0001pt;
3030 mso-line-height-rule:exactly;
3031 mso-pagination:widow-orphan;
3033 mso-shading:windowtext;
3034 mso-pattern:gray-10 auto;
3036 mso-element-frame-width:72.0pt;
3037 mso-element-frame-hspace:9.35pt;
3038 mso-element-wrap:around;
3039 mso-element-anchor-vertical:paragraph;
3040 mso-element-anchor-horizontal:margin;
3041 mso-element-top:.05pt;
3042 mso-height-rule:exactly;
3044 mso-bidi-font-size:10.0pt;
3045 font-family:Wingdings;
3046 mso-fareast-font-family:"Times New Roman";
3047 mso-bidi-font-family:"Times New Roman";
3049 letter-spacing:-.5pt;
3051 mso-bidi-font-weight:normal;}
3052 p.IndexBase, li.IndexBase, div.IndexBase
3053 {mso-style-name:"Index Base";
3055 margin-bottom:.0001pt;
3057 mso-pagination:widow-orphan;
3058 tab-stops:right 198.0pt;
3060 mso-bidi-font-size:10.0pt;
3061 font-family:Garamond;
3062 mso-fareast-font-family:"Times New Roman";
3063 mso-bidi-font-family:"Times New Roman";}
3064 p.ListBulletFirst, li.ListBulletFirst, div.ListBulletFirst
3065 {mso-style-name:"List Bullet First";
3066 mso-style-parent:"List Bullet";
3067 mso-style-next:"List Bullet";
3070 margin-bottom:8.0pt;
3073 mso-pagination:widow-orphan;
3074 mso-list:l25 level1 lfo5;
3076 font-family:"Times New Roman";
3077 mso-fareast-font-family:"Times New Roman";
3078 mso-bidi-font-family:"Times New Roman";}
3079 p.ListBulletLast, li.ListBulletLast, div.ListBulletLast
3080 {mso-style-name:"List Bullet Last";
3081 mso-style-parent:"List Bullet";
3082 mso-style-next:"Body Text";
3085 margin-bottom:12.0pt;
3088 mso-pagination:widow-orphan;
3089 mso-list:l25 level1 lfo5;
3091 font-family:"Times New Roman";
3092 mso-fareast-font-family:"Times New Roman";
3093 mso-bidi-font-family:"Times New Roman";}
3094 p.ListFirst, li.ListFirst, div.ListFirst
3095 {mso-style-name:"List First";
3096 mso-style-parent:List;
3097 mso-style-next:List;
3100 margin-bottom:4.0pt;
3102 text-indent:-18.0pt;
3103 mso-pagination:widow-orphan;
3106 font-family:"Times New Roman";
3107 mso-fareast-font-family:"Times New Roman";
3108 mso-bidi-font-family:"Times New Roman";}
3109 p.ListLast, li.ListLast, div.ListLast
3110 {mso-style-name:"List Last";
3111 mso-style-parent:List;
3112 mso-style-next:"Body Text";
3115 margin-bottom:12.0pt;
3117 text-indent:-18.0pt;
3118 mso-pagination:widow-orphan;
3121 font-family:"Times New Roman";
3122 mso-fareast-font-family:"Times New Roman";
3123 mso-bidi-font-family:"Times New Roman";}
3124 p.ListNumberFirst, li.ListNumberFirst, div.ListNumberFirst
3125 {mso-style-name:"List Number First";
3126 mso-style-parent:"List Number";
3127 mso-style-next:"List Number";
3130 margin-bottom:8.0pt;
3132 text-indent:-18.0pt;
3133 mso-pagination:widow-orphan;
3134 mso-list:l8 level1 lfo7;
3136 font-family:"Times New Roman";
3137 mso-fareast-font-family:"Times New Roman";
3138 mso-bidi-font-family:"Times New Roman";}
3139 p.ListNumberLast, li.ListNumberLast, div.ListNumberLast
3140 {mso-style-name:"List Number Last";
3141 mso-style-parent:"List Number";
3142 mso-style-next:"Body Text";
3145 margin-bottom:12.0pt;
3147 text-indent:-18.0pt;
3148 mso-pagination:widow-orphan;
3149 mso-list:l8 level1 lfo7;
3151 font-family:"Times New Roman";
3152 mso-fareast-font-family:"Times New Roman";
3153 mso-bidi-font-family:"Times New Roman";}
3154 p.PartLabel, li.PartLabel, div.PartLabel
3155 {mso-style-name:"Part Label";
3156 mso-style-link:"Part Label Char";
3157 mso-style-next:Normal;
3162 margin-bottom:.0001pt;
3165 mso-line-height-rule:exactly;
3166 mso-pagination:widow-orphan;
3168 mso-shading:windowtext;
3169 mso-pattern:gray-20 auto;
3171 mso-element-frame-width:102.25pt;
3172 mso-element-frame-hspace:9.35pt;
3173 mso-element-frame-vspace:9.35pt;
3174 mso-element-wrap:no-wrap-beside;
3175 mso-element-anchor-vertical:page;
3176 mso-element-anchor-horizontal:margin;
3177 mso-element-left:right;
3178 mso-element-top:48.3pt;
3179 mso-height-rule:exactly;
3181 mso-bidi-font-size:10.0pt;
3182 font-family:"Arial Black";
3183 mso-fareast-font-family:"Times New Roman";
3184 mso-bidi-font-family:"Times New Roman";
3187 {mso-style-name:"Part Label Char";
3188 mso-style-locked:yes;
3189 mso-style-link:"Part Label";
3190 mso-ansi-font-size:98.0pt;
3191 font-family:"Arial Black";
3192 mso-ascii-font-family:"Arial Black";
3193 mso-hansi-font-family:"Arial Black";
3195 mso-ansi-language:EN-US;
3196 mso-fareast-language:EN-US;}
3197 p.PartSubtitle, li.PartSubtitle, div.PartSubtitle
3198 {mso-style-name:"Part Subtitle";
3199 mso-style-next:"Body Text";
3202 margin-bottom:6.0pt;
3205 mso-pagination:widow-orphan;
3206 page-break-after:avoid;
3208 mso-bidi-font-size:10.0pt;
3210 mso-fareast-font-family:"Times New Roman";
3211 mso-bidi-font-family:"Times New Roman";
3212 mso-font-kerning:14.0pt;
3214 mso-bidi-font-style:normal;}
3215 p.PartTitle, li.PartTitle, div.PartTitle
3216 {mso-style-name:"Part Title";
3217 mso-style-next:"Part Label";
3219 margin-bottom:.0001pt;
3222 mso-line-height-rule:exactly;
3223 page-break-before:always;
3224 mso-pagination:widow-orphan;
3225 page-break-after:avoid;
3227 mso-shading:windowtext;
3228 mso-pattern:gray-20 auto;
3230 mso-element-frame-width:102.25pt;
3231 mso-element-frame-hspace:9.35pt;
3232 mso-element-frame-vspace:9.35pt;
3233 mso-element-wrap:no-wrap-beside;
3234 mso-element-anchor-vertical:page;
3235 mso-element-anchor-horizontal:margin;
3236 mso-element-left:right;
3237 mso-element-top:48.3pt;
3238 mso-height-rule:exactly;
3240 mso-bidi-font-size:10.0pt;
3241 font-family:"Arial Black";
3242 mso-fareast-font-family:"Times New Roman";
3243 mso-bidi-font-family:"Times New Roman";
3244 letter-spacing:-2.5pt;}
3245 p.Picture, li.Picture, div.Picture
3246 {mso-style-name:Picture;
3247 mso-style-parent:"Body Text";
3248 mso-style-next:Caption;
3251 margin-bottom:12.0pt;
3254 mso-pagination:widow-orphan;
3255 page-break-after:avoid;
3257 mso-bidi-font-size:10.0pt;
3258 font-family:Garamond;
3259 mso-fareast-font-family:"Times New Roman";
3260 mso-bidi-font-family:"Times New Roman";
3261 letter-spacing:-.25pt;}
3262 p.ReturnAddress, li.ReturnAddress, div.ReturnAddress
3263 {mso-style-name:"Return Address";
3265 margin-bottom:.0001pt;
3267 mso-pagination:widow-orphan;
3269 font-family:Garamond;
3270 mso-fareast-font-family:"Times New Roman";
3271 mso-bidi-font-family:"Times New Roman";
3272 letter-spacing:-.15pt;}
3273 p.SectionHeading, li.SectionHeading, div.SectionHeading
3274 {mso-style-name:"Section Heading";
3275 mso-style-next:"Body Text";
3277 margin-bottom:.0001pt;
3279 mso-pagination:widow-orphan;
3281 mso-bidi-font-size:10.0pt;
3282 font-family:"Arial Black";
3283 mso-fareast-font-family:"Times New Roman";
3284 mso-bidi-font-family:"Times New Roman";
3285 text-transform:uppercase;
3286 letter-spacing:3.0pt;}
3287 p.SectionLabel, li.SectionLabel, div.SectionLabel
3288 {mso-style-name:"Section Label";
3289 mso-style-next:Normal;
3292 margin-bottom:18.0pt;
3295 mso-pagination:widow-orphan;
3297 mso-bidi-font-size:10.0pt;
3298 font-family:"Arial Black";
3299 mso-fareast-font-family:"Times New Roman";
3300 mso-bidi-font-family:"Times New Roman";
3302 letter-spacing:-1.75pt;}
3303 p.SubtitleCover, li.SubtitleCover, div.SubtitleCover
3304 {mso-style-name:"Subtitle Cover";
3305 mso-style-next:Normal;
3308 margin-bottom:264.0pt;
3311 mso-line-height-rule:exactly;
3312 mso-pagination:widow-orphan;
3313 page-break-after:avoid;
3315 mso-border-top-alt:solid windowtext .75pt;
3317 mso-padding-alt:1.0pt 0cm 0cm 0cm;
3319 mso-bidi-font-size:10.0pt;
3320 font-family:Garamond;
3321 mso-fareast-font-family:"Times New Roman";
3322 mso-bidi-font-family:"Times New Roman";
3323 letter-spacing:-.75pt;
3324 mso-font-kerning:14.0pt;}
3325 p.TitleCover, li.TitleCover, div.TitleCover
3326 {mso-style-name:"Title Cover";
3327 mso-style-parent:"Heading Base";
3328 mso-style-next:"Subtitle Cover";
3330 margin-right:30.0pt;
3333 margin-bottom:.0001pt;
3336 mso-line-height-rule:exactly;
3337 mso-pagination:widow-orphan;
3339 mso-shading:windowtext;
3340 mso-pattern:gray-10 auto;
3342 mso-border-alt:solid white .75pt;
3344 mso-padding-alt:31.0pt 31.0pt 31.0pt 31.0pt;
3346 mso-bidi-font-size:10.0pt;
3347 font-family:Garamond;
3348 mso-fareast-font-family:"Times New Roman";
3349 mso-bidi-font-family:"Times New Roman";
3350 letter-spacing:-3.5pt;
3351 mso-font-kerning:14.0pt;}
3352 p.TOCBase, li.TOCBase, div.TOCBase
3353 {mso-style-name:"TOC Base";
3354 mso-style-parent:"TOC 2";
3359 margin-bottom:.0001pt;
3360 mso-pagination:widow-orphan;
3362 font-family:Cambria;
3363 mso-ascii-font-family:Cambria;
3364 mso-ascii-theme-font:minor-latin;
3365 mso-fareast-font-family:"Times New Roman";
3366 mso-hansi-font-family:Cambria;
3367 mso-hansi-theme-font:minor-latin;
3368 mso-bidi-font-family:"Times New Roman";
3370 mso-bidi-font-weight:normal;}
3371 span.Lead-inEmphasis
3372 {mso-style-name:"Lead-in Emphasis";
3373 mso-style-parent:"";
3374 mso-ansi-font-size:11.0pt;
3375 text-transform:uppercase;}
3377 {mso-style-name:Superscript;
3378 mso-style-parent:"";
3382 vertical-align:super;}
3383 p.Heading, li.Heading, div.Heading
3384 {mso-style-name:Heading;
3385 mso-style-next:Normal;
3388 margin-bottom:6.0pt;
3390 mso-pagination:none;
3391 page-break-after:avoid;
3393 mso-layout-grid-align:none;
3394 punctuation-wrap:simple;
3395 text-autospace:none;
3397 mso-bidi-font-size:10.0pt;
3398 font-family:Helvetica;
3399 mso-fareast-font-family:"Times New Roman";
3400 mso-bidi-font-family:"Times New Roman";}
3401 span.WW-Absatz-Standardschriftart
3402 {mso-style-name:WW-Absatz-Standardschriftart;
3403 mso-style-parent:"";
3404 mso-ansi-font-size:12.0pt;}
3406 {mso-style-name:"Footnote Symbol";
3407 mso-style-parent:WW-Absatz-Standardschriftart;
3408 mso-ansi-font-size:12.0pt;
3409 vertical-align:super;}
3410 span.WW-Absatz-Standardschriftart1
3411 {mso-style-name:WW-Absatz-Standardschriftart1;
3412 mso-style-parent:"";
3413 mso-ansi-font-size:12.0pt;}
3414 span.WW-FootnoteSymbol
3415 {mso-style-name:"WW-Footnote Symbol";
3416 mso-style-parent:WW-Absatz-Standardschriftart1;
3417 mso-ansi-font-size:12.0pt;
3418 vertical-align:super;}
3419 span.WW-Absatz-Standardschriftart11
3420 {mso-style-name:WW-Absatz-Standardschriftart11;
3421 mso-style-parent:"";
3422 mso-ansi-font-size:12.0pt;}
3423 span.WW-FootnoteSymbol1
3424 {mso-style-name:"WW-Footnote Symbol1";
3425 mso-style-parent:WW-Absatz-Standardschriftart11;
3426 mso-ansi-font-size:12.0pt;
3427 vertical-align:super;}
3428 span.WW-Absatz-Standardschriftart111
3429 {mso-style-name:WW-Absatz-Standardschriftart111;
3430 mso-style-parent:"";
3431 mso-ansi-font-size:12.0pt;}
3432 span.WW-FootnoteSymbol11
3433 {mso-style-name:"WW-Footnote Symbol11";
3434 mso-style-parent:WW-Absatz-Standardschriftart111;
3435 mso-ansi-font-size:12.0pt;
3436 vertical-align:super;}
3437 span.WW-Absatz-Standardschriftart1111
3438 {mso-style-name:WW-Absatz-Standardschriftart1111;
3439 mso-style-parent:"";
3440 mso-ansi-font-size:12.0pt;}
3441 span.WW-FootnoteSymbol111
3442 {mso-style-name:"WW-Footnote Symbol111";
3443 mso-style-parent:WW-Absatz-Standardschriftart1111;
3444 mso-ansi-font-size:12.0pt;
3445 vertical-align:super;}
3446 span.WW-Absatz-Standardschriftart11111
3447 {mso-style-name:WW-Absatz-Standardschriftart11111;
3448 mso-style-parent:"";
3449 mso-ansi-font-size:12.0pt;}
3450 span.WW-FootnoteSymbol1111
3451 {mso-style-name:"WW-Footnote Symbol1111";
3452 mso-style-parent:WW-Absatz-Standardschriftart11111;
3453 mso-ansi-font-size:12.0pt;
3454 vertical-align:super;}
3455 span.WW-Absatz-Standardschriftart111111
3456 {mso-style-name:WW-Absatz-Standardschriftart111111;
3457 mso-style-parent:"";
3458 mso-ansi-font-size:12.0pt;}
3459 span.WW-FootnoteSymbol11111
3460 {mso-style-name:"WW-Footnote Symbol11111";
3461 mso-style-parent:WW-Absatz-Standardschriftart111111;
3462 mso-ansi-font-size:12.0pt;
3463 vertical-align:super;}
3464 span.WW-Absatz-Standardschriftart1111111
3465 {mso-style-name:WW-Absatz-Standardschriftart1111111;
3466 mso-style-parent:"";
3467 mso-ansi-font-size:12.0pt;}
3468 span.WW-FootnoteSymbol111111
3469 {mso-style-name:"WW-Footnote Symbol111111";
3470 mso-style-parent:WW-Absatz-Standardschriftart1111111;
3471 mso-ansi-font-size:12.0pt;
3472 vertical-align:super;}
3473 span.WW-Absatz-Standardschriftart11111111
3474 {mso-style-name:WW-Absatz-Standardschriftart11111111;
3475 mso-style-parent:"";
3476 mso-ansi-font-size:12.0pt;}
3477 span.WW-FootnoteSymbol1111111
3478 {mso-style-name:"WW-Footnote Symbol1111111";
3479 mso-style-parent:WW-Absatz-Standardschriftart11111111;
3480 mso-ansi-font-size:12.0pt;
3481 vertical-align:super;}
3482 span.WW-Absatz-Standardschriftart111111111
3483 {mso-style-name:WW-Absatz-Standardschriftart111111111;
3484 mso-style-parent:"";
3485 mso-ansi-font-size:12.0pt;}
3486 span.WW-FootnoteSymbol11111111
3487 {mso-style-name:"WW-Footnote Symbol11111111";
3488 mso-style-parent:WW-Absatz-Standardschriftart111111111;
3489 mso-ansi-font-size:12.0pt;
3490 vertical-align:super;}
3492 {mso-style-name:"Endnote Symbol";
3493 mso-style-parent:"";
3494 mso-ansi-font-size:12.0pt;}
3495 span.WW-EndnoteSymbol
3496 {mso-style-name:"WW-Endnote Symbol";
3497 mso-style-parent:"";
3498 mso-ansi-font-size:12.0pt;}
3499 span.WW-EndnoteSymbol1
3500 {mso-style-name:"WW-Endnote Symbol1";
3501 mso-style-parent:"";
3502 mso-ansi-font-size:12.0pt;}
3503 span.WW-EndnoteSymbol11
3504 {mso-style-name:"WW-Endnote Symbol11";
3505 mso-style-parent:"";
3506 mso-ansi-font-size:12.0pt;}
3507 span.WW-EndnoteSymbol111
3508 {mso-style-name:"WW-Endnote Symbol111";
3509 mso-style-parent:"";
3510 mso-ansi-font-size:12.0pt;}
3511 span.WW-EndnoteSymbol1111
3512 {mso-style-name:"WW-Endnote Symbol1111";
3513 mso-style-parent:"";
3514 mso-ansi-font-size:12.0pt;}
3515 span.WW-EndnoteSymbol11111
3516 {mso-style-name:"WW-Endnote Symbol11111";
3517 mso-style-parent:"";
3518 mso-ansi-font-size:12.0pt;}
3519 span.WW-EndnoteSymbol111111
3520 {mso-style-name:"WW-Endnote Symbol111111";
3521 mso-style-parent:"";
3522 mso-ansi-font-size:12.0pt;}
3523 span.WW-EndnoteSymbol1111111
3524 {mso-style-name:"WW-Endnote Symbol1111111";
3525 mso-style-parent:"";
3526 mso-ansi-font-size:12.0pt;}
3528 {mso-style-name:"Internet link";
3529 mso-style-parent:"";
3530 mso-ansi-font-size:12.0pt;
3532 text-decoration:underline;
3533 text-underline:single;}
3534 span.WW-Internetlink
3535 {mso-style-name:"WW-Internet link";
3536 mso-style-parent:"";
3537 mso-ansi-font-size:12.0pt;
3539 text-decoration:underline;
3540 text-underline:single;}
3541 span.WW-Internetlink1
3542 {mso-style-name:"WW-Internet link1";
3543 mso-style-parent:"";
3544 mso-ansi-font-size:12.0pt;
3546 text-decoration:underline;
3547 text-underline:single;}
3548 span.WW-Internetlink11
3549 {mso-style-name:"WW-Internet link11";
3550 mso-style-parent:"";
3551 mso-ansi-font-size:12.0pt;
3553 text-decoration:underline;
3554 text-underline:single;}
3555 span.WW-Internetlink111
3556 {mso-style-name:"WW-Internet link111";
3557 mso-style-parent:"";
3558 mso-ansi-font-size:12.0pt;
3560 text-decoration:underline;
3561 text-underline:single;}
3562 span.WW-Internetlink1111
3563 {mso-style-name:"WW-Internet link1111";
3564 mso-style-parent:"";
3565 mso-ansi-font-size:12.0pt;
3567 text-decoration:underline;
3568 text-underline:single;}
3569 span.WW-Internetlink11111
3570 {mso-style-name:"WW-Internet link11111";
3571 mso-style-parent:"";
3572 mso-ansi-font-size:12.0pt;
3574 text-decoration:underline;
3575 text-underline:single;}
3576 span.WW-Internetlink111111
3577 {mso-style-name:"WW-Internet link111111";
3578 mso-style-parent:"";
3579 mso-ansi-font-size:12.0pt;
3581 text-decoration:underline;
3582 text-underline:single;}
3583 span.WW-Internetlink1111111
3584 {mso-style-name:"WW-Internet link1111111";
3585 mso-style-parent:"";
3586 mso-ansi-font-size:12.0pt;
3588 text-decoration:underline;
3589 text-underline:single;}
3590 span.VisitedInternetLink
3591 {mso-style-name:"Visited Internet Link";
3592 mso-style-parent:"";
3593 mso-ansi-font-size:12.0pt;
3595 text-decoration:underline;
3596 text-underline:single;}
3597 span.WW-VisitedInternetLink
3598 {mso-style-name:"WW-Visited Internet Link";
3599 mso-style-parent:"";
3600 mso-ansi-font-size:12.0pt;
3602 text-decoration:underline;
3603 text-underline:single;}
3604 span.WW-VisitedInternetLink1
3605 {mso-style-name:"WW-Visited Internet Link1";
3606 mso-style-parent:"";
3607 mso-ansi-font-size:12.0pt;
3609 text-decoration:underline;
3610 text-underline:single;}
3611 span.WW-VisitedInternetLink11
3612 {mso-style-name:"WW-Visited Internet Link11";
3613 mso-style-parent:"";
3614 mso-ansi-font-size:12.0pt;
3616 text-decoration:underline;
3617 text-underline:single;}
3618 span.WW-VisitedInternetLink111
3619 {mso-style-name:"WW-Visited Internet Link111";
3620 mso-style-parent:"";
3621 mso-ansi-font-size:12.0pt;
3623 text-decoration:underline;
3624 text-underline:single;}
3625 span.WW-VisitedInternetLink1111
3626 {mso-style-name:"WW-Visited Internet Link1111";
3627 mso-style-parent:"";
3628 mso-ansi-font-size:12.0pt;
3630 text-decoration:underline;
3631 text-underline:single;}
3632 span.WW-VisitedInternetLink11111
3633 {mso-style-name:"WW-Visited Internet Link11111";
3634 mso-style-parent:"";
3635 mso-ansi-font-size:12.0pt;
3637 text-decoration:underline;
3638 text-underline:single;}
3639 span.WW-VisitedInternetLink111111
3640 {mso-style-name:"WW-Visited Internet Link111111";
3641 mso-style-parent:"";
3642 mso-ansi-font-size:12.0pt;
3644 text-decoration:underline;
3645 text-underline:single;}
3646 span.WW-VisitedInternetLink1111111
3647 {mso-style-name:"WW-Visited Internet Link1111111";
3648 mso-style-parent:"";
3649 mso-ansi-font-size:12.0pt;
3651 text-decoration:underline;
3652 text-underline:single;}
3653 span.NumberingSymbols
3654 {mso-style-name:"Numbering Symbols";
3655 mso-style-parent:"";
3656 mso-ansi-font-size:12.0pt;}
3657 span.WW-NumberingSymbols
3658 {mso-style-name:"WW-Numbering Symbols";
3659 mso-style-parent:"";
3660 mso-ansi-font-size:12.0pt;}
3661 span.WW-NumberingSymbols1
3662 {mso-style-name:"WW-Numbering Symbols1";
3663 mso-style-parent:"";
3664 mso-ansi-font-size:12.0pt;}
3665 span.WW-NumberingSymbols11
3666 {mso-style-name:"WW-Numbering Symbols11";
3667 mso-style-parent:"";
3668 mso-ansi-font-size:12.0pt;}
3669 span.WW-NumberingSymbols111
3670 {mso-style-name:"WW-Numbering Symbols111";
3671 mso-style-parent:"";
3672 mso-ansi-font-size:12.0pt;}
3673 span.WW-NumberingSymbols1111
3674 {mso-style-name:"WW-Numbering Symbols1111";
3675 mso-style-parent:"";
3676 mso-ansi-font-size:12.0pt;}
3677 span.WW-NumberingSymbols11111
3678 {mso-style-name:"WW-Numbering Symbols11111";
3679 mso-style-parent:"";
3680 mso-ansi-font-size:12.0pt;}
3682 {mso-style-name:"Bullet Symbols";
3683 mso-style-parent:"";
3684 mso-ansi-font-size:9.0pt;
3685 font-family:starbats;
3686 mso-ascii-font-family:starbats;
3687 mso-hansi-font-family:starbats;}
3688 span.WW-BulletSymbols
3689 {mso-style-name:"WW-Bullet Symbols";
3690 mso-style-parent:"";
3691 mso-ansi-font-size:9.0pt;
3692 font-family:starbats;
3693 mso-ascii-font-family:starbats;
3694 mso-hansi-font-family:starbats;}
3695 span.WW-BulletSymbols1
3696 {mso-style-name:"WW-Bullet Symbols1";
3697 mso-style-parent:"";
3698 mso-ansi-font-size:9.0pt;
3699 font-family:starbats;
3700 mso-ascii-font-family:starbats;
3701 mso-hansi-font-family:starbats;}
3702 span.WW-BulletSymbols11
3703 {mso-style-name:"WW-Bullet Symbols11";
3704 mso-style-parent:"";
3705 mso-ansi-font-size:9.0pt;
3706 font-family:starbats;
3707 mso-ascii-font-family:starbats;
3708 mso-hansi-font-family:starbats;}
3709 p.Index, li.Index, div.Index
3710 {mso-style-name:Index;
3712 margin-bottom:.0001pt;
3713 mso-pagination:none;
3715 mso-layout-grid-align:none;
3716 punctuation-wrap:simple;
3717 text-autospace:none;
3719 mso-bidi-font-size:10.0pt;
3720 font-family:"Times New Roman";
3721 mso-fareast-font-family:"Times New Roman";
3722 mso-bidi-font-family:"Times New Roman";}
3723 p.ContentsHeading, li.ContentsHeading, div.ContentsHeading
3724 {mso-style-name:"Contents Heading";
3727 margin-bottom:6.0pt;
3729 mso-pagination:none;
3730 page-break-after:avoid;
3732 mso-layout-grid-align:none;
3733 punctuation-wrap:simple;
3734 text-autospace:none;
3736 mso-bidi-font-size:10.0pt;
3737 font-family:Helvetica;
3738 mso-fareast-font-family:"Times New Roman";
3739 mso-bidi-font-family:"Times New Roman";
3741 mso-bidi-font-weight:normal;}
3742 p.Tableofcontents6, li.Tableofcontents6, div.Tableofcontents6
3743 {mso-style-name:"Table of contents 6";
3744 mso-style-parent:Index;
3748 margin-left:70.75pt;
3749 margin-bottom:.0001pt;
3750 mso-pagination:none;
3752 tab-stops:right dotted 432.0pt;
3753 mso-layout-grid-align:none;
3754 punctuation-wrap:simple;
3755 text-autospace:none;
3757 mso-bidi-font-size:10.0pt;
3758 font-family:"Times New Roman";
3759 mso-fareast-font-family:"Times New Roman";
3760 mso-bidi-font-family:"Times New Roman";}
3761 p.Tableofcontents7, li.Tableofcontents7, div.Tableofcontents7
3762 {mso-style-name:"Table of contents 7";
3763 mso-style-parent:Index;
3768 margin-bottom:.0001pt;
3769 mso-pagination:none;
3771 tab-stops:right dotted 432.0pt;
3772 mso-layout-grid-align:none;
3773 punctuation-wrap:simple;
3774 text-autospace:none;
3776 mso-bidi-font-size:10.0pt;
3777 font-family:"Times New Roman";
3778 mso-fareast-font-family:"Times New Roman";
3779 mso-bidi-font-family:"Times New Roman";}
3780 p.Tableofcontents8, li.Tableofcontents8, div.Tableofcontents8
3781 {mso-style-name:"Table of contents 8";
3782 mso-style-parent:Index;
3786 margin-left:99.05pt;
3787 margin-bottom:.0001pt;
3788 mso-pagination:none;
3790 tab-stops:right dotted 432.0pt;
3791 mso-layout-grid-align:none;
3792 punctuation-wrap:simple;
3793 text-autospace:none;
3795 mso-bidi-font-size:10.0pt;
3796 font-family:"Times New Roman";
3797 mso-fareast-font-family:"Times New Roman";
3798 mso-bidi-font-family:"Times New Roman";}
3799 p.Tableofcontents9, li.Tableofcontents9, div.Tableofcontents9
3800 {mso-style-name:"Table of contents 9";
3801 mso-style-parent:Index;
3805 margin-left:113.2pt;
3806 margin-bottom:.0001pt;
3807 mso-pagination:none;
3809 tab-stops:right dotted 432.0pt;
3810 mso-layout-grid-align:none;
3811 punctuation-wrap:simple;
3812 text-autospace:none;
3814 mso-bidi-font-size:10.0pt;
3815 font-family:"Times New Roman";
3816 mso-fareast-font-family:"Times New Roman";
3817 mso-bidi-font-family:"Times New Roman";}
3818 p.Tableofcontents10, li.Tableofcontents10, div.Tableofcontents10
3819 {mso-style-name:"Table of contents 10";
3820 mso-style-parent:Index;
3824 margin-left:127.35pt;
3825 margin-bottom:.0001pt;
3826 mso-pagination:none;
3828 tab-stops:right dotted 432.0pt;
3829 mso-layout-grid-align:none;
3830 punctuation-wrap:simple;
3831 text-autospace:none;
3833 mso-bidi-font-size:10.0pt;
3834 font-family:"Times New Roman";
3835 mso-fareast-font-family:"Times New Roman";
3836 mso-bidi-font-family:"Times New Roman";}
3837 p.Textbodyindent, li.Textbodyindent, div.Textbodyindent
3838 {mso-style-name:"Text body indent";
3839 mso-style-parent:"Text body";
3843 margin-left:14.15pt;
3844 margin-bottom:.0001pt;
3846 mso-pagination:none;
3848 mso-layout-grid-align:none;
3849 punctuation-wrap:simple;
3850 text-autospace:none;
3852 mso-bidi-font-size:10.0pt;
3853 font-family:"Times New Roman";
3854 mso-fareast-font-family:"Times New Roman";
3855 mso-bidi-font-family:"Times New Roman";}
3856 p.ListContents, li.ListContents, div.ListContents
3857 {mso-style-name:"List Contents";
3862 margin-bottom:.0001pt;
3863 mso-pagination:none;
3865 mso-layout-grid-align:none;
3866 punctuation-wrap:simple;
3867 text-autospace:none;
3869 mso-bidi-font-size:10.0pt;
3870 font-family:"Times New Roman";
3871 mso-fareast-font-family:"Times New Roman";
3872 mso-bidi-font-family:"Times New Roman";}
3873 p.FAQexample, li.FAQexample, div.FAQexample
3874 {mso-style-name:FAQ_example;
3875 mso-style-parent:example;
3878 margin-bottom:12.0pt;
3882 mso-pagination:widow-orphan lines-together;
3883 page-break-after:avoid;
3884 mso-layout-grid-align:none;
3885 punctuation-wrap:simple;
3886 text-autospace:none;
3888 font-family:"Courier New";
3889 mso-fareast-font-family:"Times New Roman";
3890 mso-bidi-font-family:"Courier New";
3892 mso-bidi-font-weight:normal;}
3893 p.FAQexampleCxSpFirst, li.FAQexampleCxSpFirst, div.FAQexampleCxSpFirst
3894 {mso-style-name:FAQ_exampleCxSpFirst;
3895 mso-style-parent:example;
3896 mso-style-type:export-only;
3901 margin-bottom:.0001pt;
3904 mso-pagination:widow-orphan lines-together;
3905 page-break-after:avoid;
3906 mso-layout-grid-align:none;
3907 punctuation-wrap:simple;
3908 text-autospace:none;
3910 font-family:"Courier New";
3911 mso-fareast-font-family:"Times New Roman";
3912 mso-bidi-font-family:"Courier New";
3914 mso-bidi-font-weight:normal;}
3915 p.FAQexampleCxSpMiddle, li.FAQexampleCxSpMiddle, div.FAQexampleCxSpMiddle
3916 {mso-style-name:FAQ_exampleCxSpMiddle;
3917 mso-style-parent:example;
3918 mso-style-type:export-only;
3923 margin-bottom:.0001pt;
3926 mso-pagination:widow-orphan lines-together;
3927 page-break-after:avoid;
3928 mso-layout-grid-align:none;
3929 punctuation-wrap:simple;
3930 text-autospace:none;
3932 font-family:"Courier New";
3933 mso-fareast-font-family:"Times New Roman";
3934 mso-bidi-font-family:"Courier New";
3936 mso-bidi-font-weight:normal;}
3937 p.FAQexampleCxSpLast, li.FAQexampleCxSpLast, div.FAQexampleCxSpLast
3938 {mso-style-name:FAQ_exampleCxSpLast;
3939 mso-style-parent:example;
3940 mso-style-type:export-only;
3943 margin-bottom:12.0pt;
3947 mso-pagination:widow-orphan lines-together;
3948 page-break-after:avoid;
3949 mso-layout-grid-align:none;
3950 punctuation-wrap:simple;
3951 text-autospace:none;
3953 font-family:"Courier New";
3954 mso-fareast-font-family:"Times New Roman";
3955 mso-bidi-font-family:"Courier New";
3957 mso-bidi-font-weight:normal;}
3958 p.Firstlineindent, li.Firstlineindent, div.Firstlineindent
3959 {mso-style-name:"First line indent";
3960 mso-style-parent:"Text body";
3962 margin-bottom:.0001pt;
3964 text-indent:14.15pt;
3965 mso-pagination:none;
3967 mso-layout-grid-align:none;
3968 punctuation-wrap:simple;
3969 text-autospace:none;
3971 mso-bidi-font-size:10.0pt;
3972 font-family:"Times New Roman";
3973 mso-fareast-font-family:"Times New Roman";
3974 mso-bidi-font-family:"Times New Roman";}
3975 p.Hangingindent, li.Hangingindent, div.Hangingindent
3976 {mso-style-name:"Hanging indent";
3977 mso-style-parent:"Text body";
3982 margin-bottom:.0001pt;
3984 text-indent:-14.15pt;
3985 mso-pagination:none;
3988 mso-layout-grid-align:none;
3989 punctuation-wrap:simple;
3990 text-autospace:none;
3992 mso-bidi-font-size:10.0pt;
3993 font-family:"Times New Roman";
3994 mso-fareast-font-family:"Times New Roman";
3995 mso-bidi-font-family:"Times New Roman";}
3996 p.Numbering3, li.Numbering3, div.Numbering3
3997 {mso-style-name:"Numbering 3";
3998 mso-style-parent:List;
4001 margin-bottom:6.0pt;
4002 margin-left:42.45pt;
4004 text-indent:-14.15pt;
4005 mso-pagination:none;
4007 mso-layout-grid-align:none;
4008 punctuation-wrap:simple;
4009 text-autospace:none;
4011 mso-bidi-font-size:10.0pt;
4012 font-family:"Times New Roman";
4013 mso-fareast-font-family:"Times New Roman";
4014 mso-bidi-font-family:"Times New Roman";}
4015 p.TableContents, li.TableContents, div.TableContents
4016 {mso-style-name:"Table Contents";
4017 mso-style-parent:"Text body";
4019 margin-bottom:.0001pt;
4021 mso-pagination:none;
4023 mso-layout-grid-align:none;
4024 punctuation-wrap:simple;
4025 text-autospace:none;
4027 mso-bidi-font-size:10.0pt;
4028 font-family:"Times New Roman";
4029 mso-fareast-font-family:"Times New Roman";
4030 mso-bidi-font-family:"Times New Roman";}
4031 p.TableHeading, li.TableHeading, div.TableHeading
4032 {mso-style-name:"Table Heading";
4033 mso-style-parent:"Table Contents";
4035 margin-bottom:.0001pt;
4037 mso-pagination:none;
4039 mso-layout-grid-align:none;
4040 punctuation-wrap:simple;
4041 text-autospace:none;
4043 mso-bidi-font-size:10.0pt;
4044 font-family:"Times New Roman";
4045 mso-fareast-font-family:"Times New Roman";
4046 mso-bidi-font-family:"Times New Roman";
4048 mso-bidi-font-weight:normal;
4050 mso-bidi-font-style:normal;}
4051 p.author, li.author, div.author
4052 {mso-style-name:author;
4054 margin-bottom:.0001pt;
4056 mso-pagination:none;
4058 mso-layout-grid-align:none;
4059 punctuation-wrap:simple;
4060 text-autospace:none;
4062 mso-bidi-font-size:10.0pt;
4063 font-family:"Times New Roman";
4064 mso-fareast-font-family:"Times New Roman";
4065 mso-bidi-font-family:"Times New Roman";
4067 mso-bidi-font-weight:normal;}
4068 p.numberedlist, li.numberedlist, div.numberedlist
4069 {mso-style-name:"numbered list";
4070 mso-style-update:auto;
4071 mso-style-parent:"Heading 4";
4074 margin-bottom:3.0pt;
4076 mso-pagination:none;
4077 page-break-after:avoid;
4078 mso-outline-level:4;
4080 mso-layout-grid-align:none;
4081 punctuation-wrap:simple;
4082 text-autospace:none;
4084 mso-bidi-font-size:12.0pt;
4085 font-family:"Arial Black";
4086 mso-fareast-font-family:"Times New Roman";
4087 mso-bidi-font-family:"Courier New";
4088 letter-spacing:1.0pt;
4089 mso-ansi-language:AF;
4091 mso-bidi-font-weight:normal;
4093 mso-bidi-font-style:normal;}
4094 p.Noteboxtitle, li.Noteboxtitle, div.Noteboxtitle
4095 {mso-style-name:"Notebox\.title";
4097 margin-bottom:.0001pt;
4099 mso-pagination:none;
4101 mso-layout-grid-align:none;
4102 punctuation-wrap:simple;
4103 text-autospace:none;
4105 mso-bidi-font-size:10.0pt;
4107 mso-fareast-font-family:"Times New Roman";
4108 mso-bidi-font-family:Arial;
4110 p.noteboxexample, li.noteboxexample, div.noteboxexample
4111 {mso-style-name:"notebox\.example";
4113 margin-bottom:.0001pt;
4115 mso-pagination:none;
4117 mso-layout-grid-align:none;
4118 punctuation-wrap:simple;
4119 text-autospace:none;
4121 mso-bidi-font-size:10.0pt;
4122 font-family:"Times New Roman";
4123 mso-fareast-font-family:"Times New Roman";
4124 mso-bidi-font-family:"Times New Roman";
4126 p.noteboxbody, li.noteboxbody, div.noteboxbody
4127 {mso-style-name:"notebox\.body";
4129 margin-bottom:.0001pt;
4130 mso-pagination:none;
4132 mso-layout-grid-align:none;
4133 punctuation-wrap:simple;
4134 text-autospace:none;
4136 mso-bidi-font-size:10.0pt;
4137 font-family:"Times New Roman";
4138 mso-fareast-font-family:"Times New Roman";
4139 mso-bidi-font-family:"Times New Roman";
4141 p.Note, li.Note, div.Note
4142 {mso-style-name:Note;
4143 mso-style-update:auto;
4144 mso-style-link:"Note Char";
4147 margin-bottom:12.0pt;
4148 margin-left:42.55pt;
4150 mso-pagination:none;
4153 mso-layout-grid-align:none;
4154 punctuation-wrap:simple;
4155 text-autospace:none;
4157 mso-bidi-font-size:8.0pt;
4158 font-family:"Times New Roman";
4159 mso-fareast-font-family:"Times New Roman";
4160 mso-bidi-font-family:"Times New Roman";
4161 mso-ansi-language:EN-GB;
4163 mso-bidi-font-weight:normal;}
4165 {mso-style-name:"Note Char";
4166 mso-style-locked:yes;
4167 mso-style-link:Note;
4168 mso-bidi-font-size:8.0pt;
4169 mso-ansi-language:EN-GB;
4170 mso-fareast-language:EN-US;
4172 mso-bidi-font-weight:normal;}
4173 p.Table, li.Table, div.Table
4174 {mso-style-name:Table;
4175 mso-style-parent:Index;
4177 margin-bottom:.0001pt;
4178 mso-pagination:none;
4180 mso-layout-grid-align:none;
4181 punctuation-wrap:simple;
4182 text-autospace:none;
4184 mso-bidi-font-size:10.0pt;
4185 font-family:"Courier New";
4186 mso-fareast-font-family:"Times New Roman";
4187 mso-bidi-font-family:"Courier New";}
4188 p.flag, li.flag, div.flag
4189 {mso-style-name:flag;
4190 mso-style-parent:"Heading 4";
4193 margin-bottom:3.0pt;
4195 mso-pagination:none;
4196 page-break-after:avoid;
4197 mso-outline-level:4;
4199 mso-layout-grid-align:none;
4200 punctuation-wrap:simple;
4201 text-autospace:none;
4203 font-family:"Times New Roman";
4204 mso-fareast-font-family:"Times New Roman";
4205 mso-bidi-font-family:"Courier New";
4206 letter-spacing:1.0pt;
4207 mso-ansi-language:AF;
4209 mso-bidi-font-weight:normal;
4211 mso-bidi-font-style:normal;}
4212 p.flagusage, li.flagusage, div.flagusage
4213 {mso-style-name:"flag usage";
4214 mso-style-update:auto;
4215 mso-style-parent:example;
4218 margin-bottom:3.0pt;
4221 mso-pagination:none;
4223 mso-layout-grid-align:none;
4224 punctuation-wrap:simple;
4225 text-autospace:none;
4227 font-family:"Times New Roman";
4228 mso-fareast-font-family:"Times New Roman";
4229 mso-bidi-font-family:"Courier New";
4230 mso-ansi-language:FR;
4232 mso-bidi-font-weight:normal;}
4233 p.flagdefault, li.flagdefault, div.flagdefault
4234 {mso-style-name:"flag default";
4235 mso-style-parent:"Heading 5";
4238 margin-bottom:3.0pt;
4240 mso-pagination:none;
4241 mso-outline-level:5;
4243 mso-layout-grid-align:none;
4244 punctuation-wrap:simple;
4245 text-autospace:none;
4247 font-family:"Times New Roman";
4248 mso-fareast-font-family:"Times New Roman";
4249 mso-bidi-font-family:"Times New Roman";
4251 p.flagdescription, li.flagdescription, div.flagdescription
4252 {mso-style-name:"flag description";
4253 mso-style-update:auto;
4254 mso-style-link:"flag description Char";
4258 margin-left:42.55pt;
4259 margin-bottom:.0001pt;
4261 mso-pagination:none;
4263 mso-layout-grid-align:none;
4264 punctuation-wrap:simple;
4265 text-autospace:none;
4267 font-family:"Times New Roman";
4268 mso-fareast-font-family:"Times New Roman";
4269 mso-bidi-font-family:"Times New Roman";}
4270 span.flagdescriptionChar
4271 {mso-style-name:"flag description Char";
4272 mso-style-locked:yes;
4273 mso-style-link:"flag description";
4274 mso-ansi-language:EN-US;
4275 mso-fareast-language:EN-US;}
4276 p.flagNote, li.flagNote, div.flagNote
4277 {mso-style-name:"flag Note";
4279 margin-bottom:.0001pt;
4282 mso-pagination:none;
4284 mso-layout-grid-align:none;
4285 punctuation-wrap:simple;
4286 text-autospace:none;
4288 mso-bidi-font-size:10.0pt;
4289 font-family:"Times New Roman";
4290 mso-fareast-font-family:"Times New Roman";
4291 mso-bidi-font-family:"Times New Roman";
4293 p.flagdescriptionid1, li.flagdescriptionid1, div.flagdescriptionid1
4294 {mso-style-name:"flag description id1";
4295 mso-style-parent:"flag description";
4300 margin-bottom:.0001pt;
4302 mso-pagination:none;
4304 mso-layout-grid-align:none;
4305 punctuation-wrap:simple;
4306 text-autospace:none;
4308 font-family:"Times New Roman";
4309 mso-fareast-font-family:"Times New Roman";
4310 mso-bidi-font-family:"Times New Roman";}
4311 p.output, li.output, div.output
4312 {mso-style-name:output;
4317 margin-bottom:.0001pt;
4320 mso-pagination:none;
4322 mso-layout-grid-align:none;
4323 punctuation-wrap:simple;
4324 text-autospace:none;
4326 mso-bidi-font-size:10.0pt;
4327 font-family:Courier;
4328 mso-fareast-font-family:"Times New Roman";
4329 mso-bidi-font-family:"Times New Roman";}
4330 p.instruction, li.instruction, div.instruction
4331 {mso-style-name:instruction;
4332 mso-style-update:auto;
4333 mso-style-parent:example;
4337 margin-left:42.55pt;
4338 margin-bottom:.0001pt;
4340 mso-pagination:widow-orphan lines-together;
4341 page-break-after:avoid;
4342 mso-layout-grid-align:none;
4343 punctuation-wrap:simple;
4344 text-autospace:none;
4346 font-family:"Courier New";
4347 mso-fareast-font-family:"Times New Roman";
4348 mso-bidi-font-family:"Courier New";
4350 mso-bidi-font-weight:normal;}
4351 p.Format, li.Format, div.Format
4352 {mso-style-name:Format;
4353 mso-style-parent:example;
4356 margin-bottom:12.0pt;
4360 mso-pagination:widow-orphan lines-together;
4361 page-break-after:avoid;
4362 mso-layout-grid-align:none;
4363 punctuation-wrap:simple;
4364 text-autospace:none;
4366 font-family:"Courier New";
4367 mso-fareast-font-family:"Times New Roman";
4368 mso-bidi-font-family:"Courier New";
4369 mso-ansi-language:EN-GB;
4371 mso-bidi-font-weight:normal;}
4372 p.FormatCxSpFirst, li.FormatCxSpFirst, div.FormatCxSpFirst
4373 {mso-style-name:FormatCxSpFirst;
4374 mso-style-parent:example;
4375 mso-style-type:export-only;
4380 margin-bottom:.0001pt;
4383 mso-pagination:widow-orphan lines-together;
4384 page-break-after:avoid;
4385 mso-layout-grid-align:none;
4386 punctuation-wrap:simple;
4387 text-autospace:none;
4389 font-family:"Courier New";
4390 mso-fareast-font-family:"Times New Roman";
4391 mso-bidi-font-family:"Courier New";
4392 mso-ansi-language:EN-GB;
4394 mso-bidi-font-weight:normal;}
4395 p.FormatCxSpMiddle, li.FormatCxSpMiddle, div.FormatCxSpMiddle
4396 {mso-style-name:FormatCxSpMiddle;
4397 mso-style-parent:example;
4398 mso-style-type:export-only;
4403 margin-bottom:.0001pt;
4406 mso-pagination:widow-orphan lines-together;
4407 page-break-after:avoid;
4408 mso-layout-grid-align:none;
4409 punctuation-wrap:simple;
4410 text-autospace:none;
4412 font-family:"Courier New";
4413 mso-fareast-font-family:"Times New Roman";
4414 mso-bidi-font-family:"Courier New";
4415 mso-ansi-language:EN-GB;
4417 mso-bidi-font-weight:normal;}
4418 p.FormatCxSpLast, li.FormatCxSpLast, div.FormatCxSpLast
4419 {mso-style-name:FormatCxSpLast;
4420 mso-style-parent:example;
4421 mso-style-type:export-only;
4424 margin-bottom:12.0pt;
4428 mso-pagination:widow-orphan lines-together;
4429 page-break-after:avoid;
4430 mso-layout-grid-align:none;
4431 punctuation-wrap:simple;
4432 text-autospace:none;
4434 font-family:"Courier New";
4435 mso-fareast-font-family:"Times New Roman";
4436 mso-bidi-font-family:"Courier New";
4437 mso-ansi-language:EN-GB;
4439 mso-bidi-font-weight:normal;}
4440 p.ListinFlag, li.ListinFlag, div.ListinFlag
4441 {mso-style-name:"List in Flag";
4442 mso-style-parent:List;
4444 margin-bottom:.0001pt;
4446 mso-pagination:none;
4448 mso-layout-grid-align:none;
4449 punctuation-wrap:simple;
4450 text-autospace:none;
4452 mso-bidi-font-size:10.0pt;
4453 font-family:"Times New Roman";
4454 mso-fareast-font-family:"Times New Roman";
4455 mso-bidi-font-family:"Times New Roman";}
4456 p.example2, li.example2, div.example2
4457 {mso-style-name:example2;
4458 mso-style-parent:example;
4461 margin-bottom:12.0pt;
4465 mso-pagination:widow-orphan lines-together;
4466 page-break-after:avoid;
4467 mso-layout-grid-align:none;
4468 punctuation-wrap:simple;
4469 text-autospace:none;
4471 font-family:"Courier New";
4472 mso-fareast-font-family:"Times New Roman";
4473 mso-bidi-font-family:"Courier New";
4475 mso-bidi-font-weight:normal;}
4476 p.example2CxSpFirst, li.example2CxSpFirst, div.example2CxSpFirst
4477 {mso-style-name:example2CxSpFirst;
4478 mso-style-parent:example;
4479 mso-style-type:export-only;
4484 margin-bottom:.0001pt;
4487 mso-pagination:widow-orphan lines-together;
4488 page-break-after:avoid;
4489 mso-layout-grid-align:none;
4490 punctuation-wrap:simple;
4491 text-autospace:none;
4493 font-family:"Courier New";
4494 mso-fareast-font-family:"Times New Roman";
4495 mso-bidi-font-family:"Courier New";
4497 mso-bidi-font-weight:normal;}
4498 p.example2CxSpMiddle, li.example2CxSpMiddle, div.example2CxSpMiddle
4499 {mso-style-name:example2CxSpMiddle;
4500 mso-style-parent:example;
4501 mso-style-type:export-only;
4506 margin-bottom:.0001pt;
4509 mso-pagination:widow-orphan lines-together;
4510 page-break-after:avoid;
4511 mso-layout-grid-align:none;
4512 punctuation-wrap:simple;
4513 text-autospace:none;
4515 font-family:"Courier New";
4516 mso-fareast-font-family:"Times New Roman";
4517 mso-bidi-font-family:"Courier New";
4519 mso-bidi-font-weight:normal;}
4520 p.example2CxSpLast, li.example2CxSpLast, div.example2CxSpLast
4521 {mso-style-name:example2CxSpLast;
4522 mso-style-parent:example;
4523 mso-style-type:export-only;
4526 margin-bottom:12.0pt;
4530 mso-pagination:widow-orphan lines-together;
4531 page-break-after:avoid;
4532 mso-layout-grid-align:none;
4533 punctuation-wrap:simple;
4534 text-autospace:none;
4536 font-family:"Courier New";
4537 mso-fareast-font-family:"Times New Roman";
4538 mso-bidi-font-family:"Courier New";
4540 mso-bidi-font-weight:normal;}
4541 p.StyleNote, li.StyleNote, div.StyleNote
4542 {mso-style-name:"Style Note";
4543 mso-style-parent:Note;
4546 margin-bottom:12.0pt;
4547 margin-left:-35.45pt;
4549 mso-pagination:none;
4552 mso-layout-grid-align:none;
4553 punctuation-wrap:simple;
4554 text-autospace:none;
4556 mso-bidi-font-size:8.0pt;
4557 font-family:"Times New Roman";
4558 mso-fareast-font-family:"Times New Roman";
4559 mso-bidi-font-family:"Times New Roman";
4560 mso-ansi-language:EN-GB;
4562 p.examplefile, li.examplefile, div.examplefile
4563 {mso-style-name:example_file;
4564 mso-style-update:auto;
4567 margin-bottom:6.0pt;
4571 mso-pagination:none;
4574 mso-layout-grid-align:none;
4575 punctuation-wrap:simple;
4576 text-autospace:none;
4578 mso-border-alt:solid windowtext .5pt;
4580 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4582 font-family:"Courier New";
4583 mso-fareast-font-family:"Times New Roman";
4584 mso-bidi-font-family:"Courier New";}
4585 p.examplefileCxSpFirst, li.examplefileCxSpFirst, div.examplefileCxSpFirst
4586 {mso-style-name:example_fileCxSpFirst;
4587 mso-style-update:auto;
4588 mso-style-type:export-only;
4593 margin-bottom:.0001pt;
4596 mso-pagination:none;
4599 mso-layout-grid-align:none;
4600 punctuation-wrap:simple;
4601 text-autospace:none;
4603 mso-border-alt:solid windowtext .5pt;
4605 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4607 font-family:"Courier New";
4608 mso-fareast-font-family:"Times New Roman";
4609 mso-bidi-font-family:"Courier New";}
4610 p.examplefileCxSpMiddle, li.examplefileCxSpMiddle, div.examplefileCxSpMiddle
4611 {mso-style-name:example_fileCxSpMiddle;
4612 mso-style-update:auto;
4613 mso-style-type:export-only;
4615 margin-bottom:.0001pt;
4618 mso-pagination:none;
4621 mso-layout-grid-align:none;
4622 punctuation-wrap:simple;
4623 text-autospace:none;
4625 mso-border-alt:solid windowtext .5pt;
4627 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4629 font-family:"Courier New";
4630 mso-fareast-font-family:"Times New Roman";
4631 mso-bidi-font-family:"Courier New";}
4632 p.examplefileCxSpLast, li.examplefileCxSpLast, div.examplefileCxSpLast
4633 {mso-style-name:example_fileCxSpLast;
4634 mso-style-update:auto;
4635 mso-style-type:export-only;
4638 margin-bottom:6.0pt;
4642 mso-pagination:none;
4645 mso-layout-grid-align:none;
4646 punctuation-wrap:simple;
4647 text-autospace:none;
4649 mso-border-alt:solid windowtext .5pt;
4651 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4653 font-family:"Courier New";
4654 mso-fareast-font-family:"Times New Roman";
4655 mso-bidi-font-family:"Courier New";}
4656 p.Warning, li.Warning, div.Warning
4657 {mso-style-name:Warning;
4658 mso-style-update:auto;
4659 mso-style-link:"Warning Char";
4660 mso-margin-top-alt:auto;
4662 mso-margin-bottom-alt:auto;
4664 mso-pagination:widow-orphan;
4667 mso-border-alt:solid windowtext 1.5pt;
4669 mso-padding-alt:0cm 0cm 0cm 0cm;
4671 font-family:Garamond;
4672 mso-fareast-font-family:"Times New Roman";
4673 mso-bidi-font-family:"Times New Roman";
4675 mso-bidi-font-weight:normal;}
4677 {mso-style-name:"Warning Char";
4678 mso-style-locked:yes;
4679 mso-style-parent:"Note Char";
4680 mso-style-link:Warning;
4681 mso-bidi-font-size:8.0pt;
4682 font-family:Garamond;
4683 mso-ascii-font-family:Garamond;
4684 mso-hansi-font-family:Garamond;
4685 mso-ansi-language:EN-US;
4686 mso-fareast-language:EN-US;
4688 mso-bidi-font-weight:normal;}
4689 p.Heaing3, li.Heaing3, div.Heaing3
4690 {mso-style-name:"Heaing 3";
4691 mso-style-parent:Note;
4694 margin-bottom:12.0pt;
4695 margin-left:42.55pt;
4697 mso-pagination:none;
4700 mso-layout-grid-align:none;
4701 punctuation-wrap:simple;
4702 text-autospace:none;
4704 mso-bidi-font-size:8.0pt;
4705 font-family:"Times New Roman";
4706 mso-fareast-font-family:"Times New Roman";
4707 mso-bidi-font-family:"Times New Roman";
4708 mso-ansi-language:EN-GB;
4710 mso-bidi-font-weight:normal;}
4711 p.NormalJustified, li.NormalJustified, div.NormalJustified
4712 {mso-style-name:"Normal + Justified";
4713 mso-style-link:"Normal + Justified Char";
4715 margin-bottom:.0001pt;
4717 mso-pagination:none;
4719 mso-layout-grid-align:none;
4720 punctuation-wrap:simple;
4721 text-autospace:none;
4723 mso-bidi-font-size:10.0pt;
4724 font-family:"Times New Roman";
4725 mso-fareast-font-family:"Times New Roman";
4726 mso-bidi-font-family:"Times New Roman";
4727 mso-ansi-language:EN-GB;}
4728 span.NormalJustifiedChar
4729 {mso-style-name:"Normal + Justified Char";
4730 mso-style-locked:yes;
4731 mso-style-link:"Normal + Justified";
4732 mso-ansi-font-size:12.0pt;
4733 mso-ansi-language:EN-GB;
4734 mso-fareast-language:EN-US;}
4735 p.MyNormalID, li.MyNormalID, div.MyNormalID
4736 {mso-style-name:MyNormalID;
4737 mso-style-update:auto;
4738 mso-style-parent:"List Bullet";
4743 margin-bottom:.0001pt;
4745 mso-pagination:none;
4746 mso-list:l8 level1 lfo7;
4748 tab-stops:list 18.0pt;
4749 mso-layout-grid-align:none;
4750 punctuation-wrap:simple;
4751 text-autospace:none;
4753 mso-bidi-font-size:10.0pt;
4754 font-family:"Times New Roman";
4755 mso-fareast-font-family:"Times New Roman";
4756 mso-bidi-font-family:"Times New Roman";}
4757 p.MyExample, li.MyExample, div.MyExample
4758 {mso-style-name:MyExample;
4759 mso-style-update:auto;
4760 mso-margin-top-alt:auto;
4762 mso-margin-bottom-alt:auto;
4764 mso-pagination:none;
4767 mso-layout-grid-align:none;
4768 punctuation-wrap:simple;
4769 text-autospace:none;
4771 mso-border-top-alt:solid black .25pt;
4772 mso-border-bottom-alt:solid black .25pt;
4774 mso-padding-alt:10.0pt 0cm 10.0pt 0cm;
4776 font-family:"Courier New";
4777 mso-fareast-font-family:"Times New Roman";
4778 mso-bidi-font-family:"Times New Roman";
4780 mso-bidi-font-weight:normal;}
4781 p.Style1, li.Style1, div.Style1
4782 {mso-style-name:Style1;
4783 mso-style-update:auto;
4785 margin-bottom:.0001pt;
4786 mso-pagination:widow-orphan;
4788 mso-bidi-font-size:10.0pt;
4789 font-family:Garamond;
4790 mso-fareast-font-family:"Times New Roman";
4791 mso-bidi-font-family:"Times New Roman";
4792 mso-ansi-language:EN-GB;
4794 mso-bidi-font-weight:normal;}
4795 p.StyleHeading6Bold, li.StyleHeading6Bold, div.StyleHeading6Bold
4796 {mso-style-name:"Style Heading 6 + Bold";
4797 mso-style-update:auto;
4798 mso-style-link:"Style Heading 6 + Bold Char";
4800 margin-bottom:.0001pt;
4801 mso-pagination:widow-orphan;
4803 mso-bidi-font-size:10.0pt;
4804 font-family:Garamond;
4805 mso-fareast-font-family:"Times New Roman";
4806 mso-bidi-font-family:"Times New Roman";
4808 span.StyleHeading6BoldChar
4809 {mso-style-name:"Style Heading 6 + Bold Char";
4810 mso-style-locked:yes;
4811 mso-style-link:"Style Heading 6 + Bold";
4812 mso-ansi-font-size:8.0pt;
4813 font-family:Garamond;
4814 mso-ascii-font-family:Garamond;
4815 mso-hansi-font-family:Garamond;
4816 mso-ansi-language:EN-US;
4817 mso-fareast-language:EN-US;
4819 p.MyNormaBoldl, li.MyNormaBoldl, div.MyNormaBoldl
4820 {mso-style-name:MyNormaBoldl;
4821 mso-style-parent:MyNormal;
4822 mso-style-link:"MyNormaBoldl Char";
4825 margin-bottom:6.0pt;
4826 margin-left:42.55pt;
4828 mso-pagination:none;
4830 mso-layout-grid-align:none;
4831 punctuation-wrap:simple;
4832 text-autospace:none;
4834 font-family:"Times New Roman";
4835 mso-fareast-font-family:"Times New Roman";
4836 mso-bidi-font-family:"Courier New";
4837 mso-ansi-language:AF;}
4838 p.Mylist, li.Mylist, div.Mylist
4839 {mso-style-name:Mylist;
4840 mso-style-parent:MyNormal;
4843 margin-bottom:6.0pt;
4844 margin-left:128.7pt;
4846 text-indent:-72.0pt;
4847 mso-pagination:none;
4849 mso-layout-grid-align:none;
4850 punctuation-wrap:simple;
4851 text-autospace:none;
4853 font-family:"Times New Roman";
4854 mso-fareast-font-family:"Times New Roman";
4855 mso-bidi-font-family:"Courier New";
4856 mso-ansi-language:AF;
4858 mso-bidi-font-style:normal;}
4859 p.MyNormalBold, li.MyNormalBold, div.MyNormalBold
4860 {mso-style-name:MyNormalBold;
4861 mso-style-parent:MyNormalID;
4864 margin-bottom:12.0pt;
4867 mso-pagination:lines-together;
4868 mso-list:l8 level1 lfo7;
4869 tab-stops:list 18.0pt;
4870 mso-layout-grid-align:none;
4871 punctuation-wrap:simple;
4872 text-autospace:none;
4874 mso-bidi-font-size:10.0pt;
4875 font-family:"Times New Roman";
4876 mso-fareast-font-family:"Times New Roman";
4877 mso-bidi-font-family:"Times New Roman";}
4878 p.StyleflagdescriptionBoldItalic, li.StyleflagdescriptionBoldItalic, div.StyleflagdescriptionBoldItalic
4879 {mso-style-name:"Style flag description + Bold Italic";
4880 mso-style-update:auto;
4881 mso-style-parent:"flag description";
4882 mso-style-link:"Style flag description + Bold Italic Char";
4885 margin-bottom:3.0pt;
4886 margin-left:42.55pt;
4888 mso-pagination:none;
4890 mso-layout-grid-align:none;
4891 punctuation-wrap:simple;
4892 text-autospace:none;
4894 font-family:"Times New Roman";
4895 mso-fareast-font-family:"Times New Roman";
4896 mso-bidi-font-family:"Times New Roman";
4899 span.StyleflagdescriptionBoldItalicChar
4900 {mso-style-name:"Style flag description + Bold Italic Char";
4901 mso-style-locked:yes;
4902 mso-style-parent:"flag description Char";
4903 mso-style-link:"Style flag description + Bold Italic";
4904 mso-ansi-language:EN-US;
4905 mso-fareast-language:EN-US;
4908 p.Formula, li.Formula, div.Formula
4909 {mso-style-name:Formula;
4910 mso-style-parent:"flag description";
4914 margin-left:42.55pt;
4915 margin-bottom:.0001pt;
4917 mso-pagination:none;
4919 mso-layout-grid-align:none;
4920 punctuation-wrap:simple;
4921 text-autospace:none;
4923 font-family:"Times New Roman";
4924 mso-fareast-font-family:"Times New Roman";
4925 mso-bidi-font-family:"Times New Roman";}
4926 p.examplefilesmall, li.examplefilesmall, div.examplefilesmall
4927 {mso-style-name:example_file_small;
4928 mso-style-parent:example_file;
4931 margin-bottom:6.0pt;
4935 mso-pagination:none;
4938 mso-layout-grid-align:none;
4939 punctuation-wrap:simple;
4940 text-autospace:none;
4942 mso-border-alt:solid windowtext .5pt;
4944 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4946 mso-bidi-font-size:10.0pt;
4947 font-family:"Courier New";
4948 mso-fareast-font-family:"Times New Roman";
4949 mso-bidi-font-family:"Courier New";}
4950 p.examplefilesmallCxSpFirst, li.examplefilesmallCxSpFirst, div.examplefilesmallCxSpFirst
4951 {mso-style-name:example_file_smallCxSpFirst;
4952 mso-style-parent:example_file;
4953 mso-style-type:export-only;
4958 margin-bottom:.0001pt;
4961 mso-pagination:none;
4964 mso-layout-grid-align:none;
4965 punctuation-wrap:simple;
4966 text-autospace:none;
4968 mso-border-alt:solid windowtext .5pt;
4970 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4972 mso-bidi-font-size:10.0pt;
4973 font-family:"Courier New";
4974 mso-fareast-font-family:"Times New Roman";
4975 mso-bidi-font-family:"Courier New";}
4976 p.examplefilesmallCxSpMiddle, li.examplefilesmallCxSpMiddle, div.examplefilesmallCxSpMiddle
4977 {mso-style-name:example_file_smallCxSpMiddle;
4978 mso-style-parent:example_file;
4979 mso-style-type:export-only;
4984 margin-bottom:.0001pt;
4987 mso-pagination:none;
4990 mso-layout-grid-align:none;
4991 punctuation-wrap:simple;
4992 text-autospace:none;
4994 mso-border-alt:solid windowtext .5pt;
4996 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4998 mso-bidi-font-size:10.0pt;
4999 font-family:"Courier New";
5000 mso-fareast-font-family:"Times New Roman";
5001 mso-bidi-font-family:"Courier New";}
5002 p.examplefilesmallCxSpLast, li.examplefilesmallCxSpLast, div.examplefilesmallCxSpLast
5003 {mso-style-name:example_file_smallCxSpLast;
5004 mso-style-parent:example_file;
5005 mso-style-type:export-only;
5008 margin-bottom:6.0pt;
5012 mso-pagination:none;
5015 mso-layout-grid-align:none;
5016 punctuation-wrap:simple;
5017 text-autospace:none;
5019 mso-border-alt:solid windowtext .5pt;
5021 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
5023 mso-bidi-font-size:10.0pt;
5024 font-family:"Courier New";
5025 mso-fareast-font-family:"Times New Roman";
5026 mso-bidi-font-family:"Courier New";}
5027 p.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, li.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, div.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut
5028 {mso-style-name:"Style notebox\.body + Bold Not Italic Box\: \(Single solid line Aut\.\.\.";
5029 mso-style-parent:"notebox\.body";
5031 margin-bottom:.0001pt;
5032 mso-pagination:none;
5035 mso-layout-grid-align:none;
5036 punctuation-wrap:simple;
5037 text-autospace:none;
5039 mso-border-alt:solid windowtext 1.5pt;
5041 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
5043 mso-bidi-font-size:10.0pt;
5044 font-family:"Times New Roman";
5045 mso-fareast-font-family:"Times New Roman";
5046 mso-bidi-font-family:"Times New Roman";
5048 p.MyNormalJustified, li.MyNormalJustified, div.MyNormalJustified
5049 {mso-style-name:MyNormalJustified;
5050 mso-style-parent:MyNormal;
5053 margin-bottom:6.0pt;
5054 margin-left:42.55pt;
5055 mso-pagination:none;
5057 mso-layout-grid-align:none;
5058 punctuation-wrap:simple;
5059 text-autospace:none;
5061 font-family:"Times New Roman";
5062 mso-fareast-font-family:"Times New Roman";
5063 mso-bidi-font-family:"Courier New";}
5064 p.flagheading2, li.flagheading2, div.flagheading2
5065 {mso-style-name:"flag heading 2";
5066 mso-style-update:auto;
5067 mso-style-parent:"flag description";
5072 margin-bottom:.0001pt;
5074 mso-pagination:none;
5076 mso-layout-grid-align:none;
5077 punctuation-wrap:simple;
5078 text-autospace:none;
5080 font-family:"Times New Roman";
5081 mso-fareast-font-family:"Times New Roman";
5082 mso-bidi-font-family:"Times New Roman";
5084 mso-bidi-font-weight:normal;
5086 mso-bidi-font-style:normal;
5087 text-decoration:underline;
5088 text-underline:single;}
5089 p.example1, li.example1, div.example1
5090 {mso-style-name:example1;
5091 mso-style-parent:example2;
5094 margin-bottom:12.0pt;
5098 mso-pagination:widow-orphan lines-together;
5099 page-break-after:avoid;
5100 mso-layout-grid-align:none;
5101 punctuation-wrap:simple;
5102 text-autospace:none;
5104 font-family:"Courier New";
5105 mso-fareast-font-family:"Times New Roman";
5106 mso-bidi-font-family:"Courier New";
5108 mso-bidi-font-weight:normal;}
5109 p.example1CxSpFirst, li.example1CxSpFirst, div.example1CxSpFirst
5110 {mso-style-name:example1CxSpFirst;
5111 mso-style-parent:example2;
5112 mso-style-type:export-only;
5117 margin-bottom:.0001pt;
5120 mso-pagination:widow-orphan lines-together;
5121 page-break-after:avoid;
5122 mso-layout-grid-align:none;
5123 punctuation-wrap:simple;
5124 text-autospace:none;
5126 font-family:"Courier New";
5127 mso-fareast-font-family:"Times New Roman";
5128 mso-bidi-font-family:"Courier New";
5130 mso-bidi-font-weight:normal;}
5131 p.example1CxSpMiddle, li.example1CxSpMiddle, div.example1CxSpMiddle
5132 {mso-style-name:example1CxSpMiddle;
5133 mso-style-parent:example2;
5134 mso-style-type:export-only;
5139 margin-bottom:.0001pt;
5142 mso-pagination:widow-orphan lines-together;
5143 page-break-after:avoid;
5144 mso-layout-grid-align:none;
5145 punctuation-wrap:simple;
5146 text-autospace:none;
5148 font-family:"Courier New";
5149 mso-fareast-font-family:"Times New Roman";
5150 mso-bidi-font-family:"Courier New";
5152 mso-bidi-font-weight:normal;}
5153 p.example1CxSpLast, li.example1CxSpLast, div.example1CxSpLast
5154 {mso-style-name:example1CxSpLast;
5155 mso-style-parent:example2;
5156 mso-style-type:export-only;
5159 margin-bottom:12.0pt;
5163 mso-pagination:widow-orphan lines-together;
5164 page-break-after:avoid;
5165 mso-layout-grid-align:none;
5166 punctuation-wrap:simple;
5167 text-autospace:none;
5169 font-family:"Courier New";
5170 mso-fareast-font-family:"Times New Roman";
5171 mso-bidi-font-family:"Courier New";
5173 mso-bidi-font-weight:normal;}
5174 span.MyNormaBoldlChar
5175 {mso-style-name:"MyNormaBoldl Char";
5176 mso-style-locked:yes;
5177 mso-style-parent:"MyNormal Char";
5178 mso-style-link:MyNormaBoldl;
5179 mso-ansi-font-size:11.0pt;
5180 mso-bidi-font-size:11.0pt;
5181 font-family:"Courier New";
5182 mso-ascii-font-family:"Courier New";
5183 mso-hansi-font-family:"Courier New";
5184 mso-bidi-font-family:"Courier New";
5185 mso-ansi-language:AF;
5186 mso-fareast-language:EN-US;}
5187 p.MyNormal2, li.MyNormal2, div.MyNormal2
5188 {mso-style-name:MyNormal2;
5189 mso-style-parent:MyNormal;
5192 margin-bottom:6.0pt;
5193 margin-left:42.55pt;
5195 mso-pagination:none;
5197 mso-layout-grid-align:none;
5198 punctuation-wrap:simple;
5199 text-autospace:none;
5201 font-family:"Times New Roman";
5202 mso-fareast-font-family:"Times New Roman";
5203 mso-bidi-font-family:"Courier New";
5204 mso-ansi-language:AF;}
5206 {mso-style-type:export-only;
5208 text-decoration:underline;
5209 text-underline:single;
5212 {mso-style-type:export-only;
5214 text-decoration:line-through;
5217 {mso-style-type:export-only;
5220 /* Page Definitions */
5222 {mso-footnote-separator:url(":t_coffee_technical_files:header.htm") fs;
5223 mso-footnote-continuation-separator:url(":t_coffee_technical_files:header.htm") fcs;
5224 mso-endnote-separator:url(":t_coffee_technical_files:header.htm") es;
5225 mso-endnote-continuation-separator:url(":t_coffee_technical_files:header.htm") ecs;}
5227 {size:21.0cm 842.0pt;
5228 margin:48.0pt 48.0pt 48.0pt 48.0pt;
5229 mso-header-margin:0cm;
5230 mso-footer-margin:0cm;
5233 mso-footer:url(":t_coffee_technical_files:header.htm") f1;
5234 mso-paper-source:0;}
5238 {size:21.0cm 842.0pt;
5239 margin:90.0pt 60.0pt 90.0pt 60.0pt;
5240 mso-header-margin:48.0pt;
5241 mso-footer-margin:48.0pt;
5242 mso-page-numbers:roman-lower 1;
5244 mso-footer:url(":t_coffee_technical_files:header.htm") f1;
5245 mso-first-footer:url(":t_coffee_technical_files:header.htm") ff2;
5246 mso-paper-source:0;}
5250 {size:21.0cm 842.0pt;
5251 margin:90.0pt 60.0pt 90.0pt 60.0pt;
5252 mso-header-margin:48.0pt;
5253 mso-footer-margin:48.0pt;
5255 mso-header:url(":t_coffee_technical_files:header.htm") h3;
5256 mso-footer:url(":t_coffee_technical_files:header.htm") f3;
5257 mso-first-header:url(":t_coffee_technical_files:header.htm") fh3;
5258 mso-first-footer:url(":t_coffee_technical_files:header.htm") ff3;
5259 mso-paper-source:0;}
5263 {size:21.0cm 842.0pt;
5264 margin:72.0pt 90.0pt 72.0pt 90.0pt;
5265 mso-header-margin:36.0pt;
5266 mso-footer-margin:36.0pt;
5267 mso-header:url(":t_coffee_technical_files:header.htm") h4;
5268 mso-footer:url(":t_coffee_technical_files:header.htm") f4;
5269 mso-first-header:url(":t_coffee_technical_files:header.htm") fh4;
5270 mso-first-footer:url(":t_coffee_technical_files:header.htm") ff3;
5271 mso-paper-source:0;}
5274 /* List Definitions */
5277 mso-list-type:simple;
5278 mso-list-template-ids:243462170;}
5280 {mso-level-style-link:"List Number 3";
5281 mso-level-tab-stop:90.0pt;
5282 mso-level-number-position:left;
5284 text-indent:-18.0pt;}
5287 mso-list-type:simple;
5288 mso-list-template-ids:579796312;}
5290 {mso-level-style-link:"List Number 2";
5291 mso-level-tab-stop:72.0pt;
5292 mso-level-number-position:left;
5294 text-indent:-18.0pt;}
5297 mso-list-type:simple;
5298 mso-list-template-ids:-525153058;}
5300 {mso-level-style-link:"List Bullet 5";
5301 mso-level-tab-stop:54.0pt;
5302 mso-level-number-position:left;
5304 text-indent:-18.0pt;}
5307 mso-list-type:simple;
5308 mso-list-template-ids:1970563230;}
5310 {mso-level-style-link:"List Bullet 4";
5311 mso-level-tab-stop:36.0pt;
5312 mso-level-number-position:left;
5313 text-indent:-18.0pt;}
5316 mso-list-type:simple;
5317 mso-list-template-ids:-118980482;}
5319 {mso-level-number-format:bullet;
5320 mso-level-style-link:"List Bullet 3";
5321 mso-level-text:\F0B7;
5322 mso-level-tab-stop:90.0pt;
5323 mso-level-number-position:left;
5325 text-indent:-18.0pt;
5326 font-family:Symbol;}
5329 mso-list-type:simple;
5330 mso-list-template-ids:-1465100272;}
5332 {mso-level-number-format:bullet;
5333 mso-level-style-link:"List Bullet 2";
5334 mso-level-text:\F0B7;
5335 mso-level-tab-stop:72.0pt;
5336 mso-level-number-position:left;
5338 text-indent:-18.0pt;
5339 font-family:Symbol;}
5342 mso-list-type:simple;
5343 mso-list-template-ids:-368430812;}
5345 {mso-level-number-format:bullet;
5346 mso-level-style-link:"List 5";
5347 mso-level-text:\F0B7;
5348 mso-level-tab-stop:54.0pt;
5349 mso-level-number-position:left;
5351 text-indent:-18.0pt;
5352 font-family:Symbol;}
5355 mso-list-type:simple;
5356 mso-list-template-ids:-706941758;}
5358 {mso-level-number-format:bullet;
5359 mso-level-style-link:"List 4";
5360 mso-level-text:\F0B7;
5361 mso-level-tab-stop:36.0pt;
5362 mso-level-number-position:left;
5363 text-indent:-18.0pt;
5364 font-family:Symbol;}
5367 mso-list-type:simple;
5368 mso-list-template-ids:1576020400;}
5370 {mso-level-style-link:"Plain Text";
5371 mso-level-tab-stop:18.0pt;
5372 mso-level-number-position:left;
5374 text-indent:-18.0pt;}
5377 mso-list-type:simple;
5378 mso-list-template-ids:96769246;}
5380 {mso-level-number-format:bullet;
5381 mso-level-style-link:"Text body Char";
5382 mso-level-text:\F0B7;
5383 mso-level-tab-stop:18.0pt;
5384 mso-level-number-position:left;
5386 text-indent:-18.0pt;
5387 font-family:Symbol;}
5390 mso-list-template-ids:-1557078836;}
5392 {mso-level-number-format:none;
5393 mso-level-suffix:none;
5395 mso-level-tab-stop:none;
5396 mso-level-number-position:left;
5400 {mso-level-number-format:none;
5402 mso-level-tab-stop:none;
5403 mso-level-number-position:left;
5404 mso-level-legacy:yes;
5405 mso-level-legacy-indent:0cm;
5406 mso-level-legacy-space:0cm;
5410 {mso-level-number-format:none;
5412 mso-level-tab-stop:none;
5413 mso-level-number-position:left;
5414 mso-level-legacy:yes;
5415 mso-level-legacy-indent:0cm;
5416 mso-level-legacy-space:0cm;
5420 {mso-level-number-format:none;
5422 mso-level-tab-stop:none;
5423 mso-level-number-position:left;
5424 mso-level-legacy:yes;
5425 mso-level-legacy-indent:0cm;
5426 mso-level-legacy-space:0cm;
5429 mso-ansi-language:EN-GB;}
5431 {mso-level-start-at:0;
5432 mso-level-number-format:none;
5434 mso-level-tab-stop:none;
5435 mso-level-number-position:left;
5439 {mso-level-start-at:0;
5440 mso-level-number-format:none;
5442 mso-level-tab-stop:none;
5443 mso-level-number-position:left;
5447 {mso-level-start-at:0;
5448 mso-level-number-format:none;
5450 mso-level-tab-stop:none;
5451 mso-level-number-position:left;
5455 {mso-level-start-at:0;
5456 mso-level-number-format:none;
5458 mso-level-tab-stop:none;
5459 mso-level-number-position:left;
5463 {mso-level-start-at:0;
5464 mso-level-number-format:none;
5466 mso-level-tab-stop:none;
5467 mso-level-number-position:left;
5472 mso-list-type:simple;
5473 mso-list-template-ids:-1;}
5475 {mso-level-start-at:0;
5477 mso-level-tab-stop:none;
5478 mso-level-number-position:left;
5482 {mso-list-id:16198800;
5483 mso-list-type:hybrid;
5484 mso-list-template-ids:-1589361750 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
5486 {mso-level-tab-stop:78.55pt;
5487 mso-level-number-position:left;
5488 margin-left:78.55pt;
5489 text-indent:-18.0pt;}
5491 {mso-level-number-format:alpha-lower;
5492 mso-level-tab-stop:114.55pt;
5493 mso-level-number-position:left;
5494 margin-left:114.55pt;
5495 text-indent:-18.0pt;}
5497 {mso-list-id:31855817;
5498 mso-list-type:hybrid;
5499 mso-list-template-ids:1137623166 -1 -1 -1 -1 -1 -1 -1 -1 -1;}
5501 {mso-level-number-format:bullet;
5502 mso-level-text:\F0A7;
5503 mso-level-tab-stop:108.0pt;
5504 mso-level-number-position:left;
5505 margin-left:108.0pt;
5506 text-indent:-18.0pt;
5507 font-family:Wingdings;}
5509 {mso-list-id:351080084;
5510 mso-list-template-ids:1670832864;}
5512 {mso-level-number-format:bullet;
5513 mso-level-text:\F0B7;
5514 mso-level-tab-stop:36.0pt;
5515 mso-level-number-position:left;
5516 text-indent:-18.0pt;
5517 mso-ansi-font-size:10.0pt;
5518 font-family:Symbol;}
5520 {mso-level-tab-stop:72.0pt;
5521 mso-level-number-position:left;
5522 text-indent:-18.0pt;}
5524 {mso-list-id:429860257;
5525 mso-list-type:simple;
5526 mso-list-template-ids:-1193904264;}
5528 {mso-level-tab-stop:none;
5529 mso-level-number-position:left;
5530 mso-level-legacy:yes;
5531 mso-level-legacy-indent:18.0pt;
5532 mso-level-legacy-space:0cm;
5533 margin-right:36.0pt;
5534 text-indent:-18.0pt;
5535 mso-ansi-font-size:10.0pt;
5536 mso-ascii-font-family:"Arial Black";
5537 mso-hansi-font-family:"Arial Black";}
5539 {mso-list-id:873344605;
5540 mso-list-template-ids:1828727762;}
5542 {mso-level-number-format:bullet;
5543 mso-level-text:\F0A7;
5544 mso-level-tab-stop:18.0pt;
5545 mso-level-number-position:left;
5547 text-indent:-18.0pt;
5548 font-family:Wingdings;}
5550 {mso-level-number-format:none;
5552 mso-level-tab-stop:none;
5553 mso-level-number-position:left;
5554 mso-level-legacy:yes;
5555 mso-level-legacy-indent:0cm;
5556 mso-level-legacy-space:0cm;
5560 {mso-level-number-format:none;
5562 mso-level-tab-stop:none;
5563 mso-level-number-position:left;
5564 mso-level-legacy:yes;
5565 mso-level-legacy-indent:0cm;
5566 mso-level-legacy-space:0cm;
5570 {mso-level-number-format:none;
5572 mso-level-tab-stop:none;
5573 mso-level-number-position:left;
5574 mso-level-legacy:yes;
5575 mso-level-legacy-indent:0cm;
5576 mso-level-legacy-space:0cm;
5580 {mso-level-start-at:0;
5581 mso-level-number-format:none;
5583 mso-level-tab-stop:none;
5584 mso-level-number-position:left;
5588 {mso-level-start-at:0;
5589 mso-level-number-format:none;
5591 mso-level-tab-stop:none;
5592 mso-level-number-position:left;
5596 {mso-level-start-at:0;
5597 mso-level-number-format:none;
5599 mso-level-tab-stop:none;
5600 mso-level-number-position:left;
5604 {mso-level-start-at:0;
5605 mso-level-number-format:none;
5607 mso-level-tab-stop:none;
5608 mso-level-number-position:left;
5612 {mso-level-start-at:0;
5613 mso-level-number-format:none;
5615 mso-level-tab-stop:none;
5616 mso-level-number-position:left;
5620 {mso-list-id:934939961;
5621 mso-list-type:hybrid;
5622 mso-list-template-ids:-467735746 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
5624 {mso-level-tab-stop:78.55pt;
5625 mso-level-number-position:left;
5626 margin-left:78.55pt;
5627 text-indent:-18.0pt;}
5629 {mso-list-id:941451051;
5630 mso-list-type:hybrid;
5631 mso-list-template-ids:1232603580 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
5633 {mso-level-tab-stop:78.55pt;
5634 mso-level-number-position:left;
5635 margin-left:78.55pt;
5636 text-indent:-18.0pt;}
5638 {mso-list-id:964848167;
5639 mso-list-template-ids:1912510992;}
5641 {mso-level-number-format:bullet;
5642 mso-level-text:\F0B7;
5643 mso-level-tab-stop:36.0pt;
5644 mso-level-number-position:left;
5645 text-indent:-18.0pt;
5646 mso-ansi-font-size:10.0pt;
5647 font-family:Symbol;}
5649 {mso-level-number-format:bullet;
5651 mso-level-tab-stop:72.0pt;
5652 mso-level-number-position:left;
5653 text-indent:-18.0pt;
5654 mso-ansi-font-size:10.0pt;
5655 font-family:"Courier New";}
5657 {mso-level-number-format:bullet;
5658 mso-level-text:\F0A7;
5659 mso-level-tab-stop:108.0pt;
5660 mso-level-number-position:left;
5661 text-indent:-18.0pt;
5662 mso-ansi-font-size:10.0pt;
5663 font-family:Wingdings;}
5665 {mso-list-id:976836001;
5666 mso-list-type:hybrid;
5667 mso-list-template-ids:-1213013906 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
5669 {mso-level-tab-stop:78.55pt;
5670 mso-level-number-position:left;
5671 margin-left:78.55pt;
5672 text-indent:-18.0pt;}
5674 {mso-list-id:1112475268;
5675 mso-list-type:hybrid;
5676 mso-list-template-ids:1170372944 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
5678 {mso-level-tab-stop:78.55pt;
5679 mso-level-number-position:left;
5680 margin-left:78.55pt;
5681 text-indent:-18.0pt;}
5683 {mso-list-id:1280378370;
5684 mso-list-type:simple;
5685 mso-list-template-ids:-247183560;}
5687 {mso-level-number-format:bullet;
5688 mso-level-style-link:"List Bullet 3";
5689 mso-level-text:\F0A7;
5690 mso-level-tab-stop:18.0pt;
5691 mso-level-number-position:left;
5693 margin-right:18.0pt;
5696 margin-bottom:.0001pt;
5697 text-indent:-18.0pt;
5698 font-family:Wingdings;}
5700 {mso-list-id:1469779017;
5701 mso-list-type:simple;
5702 mso-list-template-ids:-1193904264;}
5704 {mso-level-tab-stop:none;
5705 mso-level-number-position:left;
5706 mso-level-legacy:yes;
5707 mso-level-legacy-indent:18.0pt;
5708 mso-level-legacy-space:0cm;
5709 margin-right:36.0pt;
5710 text-indent:-18.0pt;
5711 mso-ansi-font-size:10.0pt;
5712 mso-ascii-font-family:"Arial Black";
5713 mso-hansi-font-family:"Arial Black";}
5715 {mso-list-id:1589343465;
5716 mso-list-template-ids:1670832864;}
5718 {mso-level-number-format:bullet;
5719 mso-level-text:\F0B7;
5720 mso-level-tab-stop:36.0pt;
5721 mso-level-number-position:left;
5722 text-indent:-18.0pt;
5723 mso-ansi-font-size:10.0pt;
5724 font-family:Symbol;}
5726 {mso-level-tab-stop:72.0pt;
5727 mso-level-number-position:left;
5728 text-indent:-18.0pt;}
5730 {mso-list-id:1598251408;
5731 mso-list-type:simple;
5732 mso-list-template-ids:-674336410;}
5734 {mso-level-number-format:bullet;
5735 mso-level-style-link:"Text body Char";
5736 mso-level-text:\F0A7;
5737 mso-level-tab-stop:18.0pt;
5738 mso-level-number-position:left;
5740 margin-right:18.0pt;
5743 margin-bottom:.0001pt;
5744 text-indent:-18.0pt;
5745 font-family:Wingdings;}
5747 {mso-list-id:1649675689;
5748 mso-list-type:simple;
5749 mso-list-template-ids:-1193904264;}
5751 {mso-level-tab-stop:none;
5752 mso-level-number-position:left;
5753 mso-level-legacy:yes;
5754 mso-level-legacy-indent:18.0pt;
5755 mso-level-legacy-space:0cm;
5756 margin-right:36.0pt;
5757 text-indent:-18.0pt;
5758 mso-ansi-font-size:10.0pt;
5759 mso-ascii-font-family:"Arial Black";
5760 mso-hansi-font-family:"Arial Black";}
5762 {mso-list-id:2072076493;
5763 mso-list-type:hybrid;
5764 mso-list-template-ids:-1431952502 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
5766 {mso-level-tab-stop:78.55pt;
5767 mso-level-number-position:left;
5768 margin-left:78.55pt;
5769 text-indent:-18.0pt;}
5770 @list l11:level1 lfo19
5771 {mso-level-number-format:bullet;
5772 mso-level-numbering:continue;
5773 mso-level-text:\F031;
5774 mso-level-tab-stop:none;
5775 mso-level-number-position:left;
5776 mso-level-legacy:yes;
5777 mso-level-legacy-indent:18.0pt;
5778 mso-level-legacy-space:0cm;
5780 margin-right:18.0pt;
5783 margin-bottom:.0001pt;
5784 text-indent:-18.0pt;
5785 mso-ansi-font-size:11.0pt;
5786 mso-ascii-font-family:Wingdings;
5787 mso-hansi-font-family:Wingdings;}
5788 @list l11:level1 lfo20
5789 {mso-level-number-format:bullet;
5790 mso-level-numbering:continue;
5791 mso-level-text:\F021;
5792 mso-level-tab-stop:none;
5793 mso-level-number-position:left;
5794 mso-level-legacy:yes;
5795 mso-level-legacy-indent:18.0pt;
5796 mso-level-legacy-space:0cm;
5798 margin-right:18.0pt;
5801 margin-bottom:.0001pt;
5802 text-indent:-18.0pt;
5803 mso-ansi-font-size:12.0pt;
5804 mso-ascii-font-family:Wingdings;
5805 mso-hansi-font-family:Wingdings;}
5806 @list l11:level1 lfo21
5807 {mso-level-number-format:bullet;
5808 mso-level-numbering:continue;
5809 mso-level-text:\F03A;
5810 mso-level-tab-stop:none;
5811 mso-level-number-position:left;
5812 mso-level-legacy:yes;
5813 mso-level-legacy-indent:18.0pt;
5814 mso-level-legacy-space:0cm;
5816 margin-right:18.0pt;
5819 margin-bottom:.0001pt;
5820 text-indent:-18.0pt;
5821 mso-ansi-font-size:11.0pt;
5822 mso-ascii-font-family:Wingdings;
5823 mso-hansi-font-family:Wingdings;}
5824 @list l11:level1 lfo22
5825 {mso-level-number-format:bullet;
5826 mso-level-numbering:continue;
5827 mso-level-text:\F026;
5828 mso-level-tab-stop:none;
5829 mso-level-number-position:left;
5830 mso-level-legacy:yes;
5831 mso-level-legacy-indent:18.0pt;
5832 mso-level-legacy-space:0cm;
5834 margin-right:18.0pt;
5837 margin-bottom:.0001pt;
5838 text-indent:-18.0pt;
5839 mso-ansi-font-size:10.0pt;
5840 mso-ascii-font-family:Wingdings;
5841 mso-hansi-font-family:Wingdings;}
5842 @list l11:level1 lfo23
5843 {mso-level-number-format:bullet;
5844 mso-level-numbering:continue;
5845 mso-level-text:\F0B7;
5846 mso-level-tab-stop:none;
5847 mso-level-number-position:left;
5848 mso-level-legacy:yes;
5849 mso-level-legacy-indent:18.0pt;
5850 mso-level-legacy-space:0cm;
5852 margin-right:36.0pt;
5855 margin-bottom:.0001pt;
5856 text-indent:-18.0pt;
5857 mso-ansi-font-size:14.0pt;
5858 mso-ascii-font-family:Symbol;
5859 mso-hansi-font-family:Symbol;}
5860 @list l11:level1 lfo24
5861 {mso-level-number-format:bullet;
5862 mso-level-numbering:continue;
5863 mso-level-text:\F0B7;
5864 mso-level-tab-stop:none;
5865 mso-level-number-position:left;
5866 mso-level-legacy:yes;
5867 mso-level-legacy-indent:18.0pt;
5868 mso-level-legacy-space:0cm;
5870 margin-right:36.0pt;
5873 margin-bottom:.0001pt;
5874 text-indent:-18.0pt;
5875 mso-ansi-font-size:14.0pt;
5876 mso-ascii-font-family:Symbol;
5877 mso-hansi-font-family:Symbol;}
5879 {margin-bottom:0cm;}
5881 {margin-bottom:0cm;}
5884 <!--[if gte mso 10]>
5886 /* Style Definitions */
5887 table.MsoNormalTable
5888 {mso-style-name:"Table Normal";
5889 mso-tstyle-rowband-size:0;
5890 mso-tstyle-colband-size:0;
5891 mso-style-noshow:yes;
5892 mso-style-parent:"";
5893 mso-padding-alt:0cm 5.4pt 0cm 5.4pt;
5894 mso-para-margin:0cm;
5895 mso-para-margin-bottom:.0001pt;
5896 mso-pagination:widow-orphan;
5898 font-family:"Times New Roman";}
5900 <![endif]--><!--[if gte mso 9]><xml>
5901 <o:shapedefaults v:ext="edit" spidmax="2050"/>
5902 </xml><![endif]--><!--[if gte mso 9]><xml>
5903 <o:shapelayout v:ext="edit">
5904 <o:idmap v:ext="edit" data="1"/>
5905 </o:shapelayout></xml><![endif]-->
5908 <body lang=EN-US link=blue vlink=purple style='tab-interval:35.4pt'>
5910 <div class=Section1>
5912 <div style='mso-element:frame;mso-element-wrap:no-wrap-beside;mso-height-rule:
5915 <table cellspacing=0 cellpadding=0 hspace=0 vspace=0 width=112 align=right>
5917 <td valign=top style='padding-top:9.35pt;padding-right:9.35pt;padding-bottom:
5918 9.35pt;padding-left:9.35pt'>
5919 <p class=PartTitle>Technical</p>
5926 <![if !supportTextWrap]><br clear=ALL>
5929 <p class=CompanyName><span style='font-size:14.0pt'>Centre National De LA
5930 Recherche scientifique (France)<br>
5931 CeNTRO De REGULACIO GENOMICA (SPAIN)<o:p></o:p></span></p>
5933 <div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;
5934 mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0cm 0cm 0cm'>
5936 <p class=SubtitleCover>Cédric Notredame<br>
5941 <div style='mso-element:para-border-div;border:solid white 1.0pt;mso-border-alt:
5942 solid white .75pt;padding:31.0pt 31.0pt 31.0pt 31.0pt;background:#E5E5E5;
5943 mso-shading:windowtext;mso-pattern:gray-10 auto'>
5945 <p class=TitleCover style='margin:0cm;margin-bottom:.0001pt;background:#E5E5E5;
5946 mso-shading:windowtext;mso-pattern:gray-10 auto'>T-Coffee:<br>
5947 Technical Documentation</p>
5951 <div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;
5952 mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0cm 0cm 0cm'>
5954 <p class=SubtitleCover><o:p> </o:p></p>
5960 <span style='font-size:72.0pt;mso-bidi-font-size:10.0pt;font-family:Garamond;
5961 mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
5962 letter-spacing:-3.5pt;mso-font-kerning:14.0pt;mso-ansi-language:EN-US;
5963 mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:always;
5964 mso-break-type:section-break'>
5967 <div class=Section2>
5969 <div style='mso-element:para-border-div;border:none;border-bottom:solid gray 1.0pt;
5970 mso-border-bottom-alt:solid gray .75pt;padding:0cm 0cm 14.0pt 0cm'>
5972 <p class=MsoTitle>T-Coffee Technical Documentation<br>
5973 (Version 8.96, July 2010)<br>
5976 T-Coffee, seq_reformat<br>
5977 <span style="mso-spacerun: yes"> </span>PSI-Coffee, 3D-Coffee, Expresso, M-Coffee,
5978 R-Coffee, APDB, iRMSD, T-RMSD</p>
5982 <p class=ReturnAddress><span style='font-family:Symbol;mso-ascii-font-family:
5983 Garamond;mso-hansi-font-family:Garamond;mso-char-type:symbol;mso-symbol-font-family:
5984 Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>ã</span></span>
5985 Cédric Notredame, Centro de Regulacio Genomica, Centre National de la Recherche
5986 Scientifique, France<span style='letter-spacing:0pt'><o:p></o:p></span></p>
5990 <span style='font-size:8.0pt;mso-bidi-font-size:10.0pt;font-family:Garamond;
5991 mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
5992 mso-ansi-language:EN-US;mso-fareast-language:EN-US'><br clear=ALL
5993 style='page-break-before:always;mso-break-type:section-break'>
5996 <div class=Section3>
5998 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><!--[if supportFields]><span
5999 style='mso-element:field-begin'></span><span style="mso-spacerun:
6000 yes"> </span>TOC <span style='mso-element:field-separator'></span><![endif]--><span
6001 style='mso-no-proof:yes'>T-Coffee is distributed under the Gnu Public License<span
6002 style='mso-tab-count:1 dotted'>................................................................. </span></span><!--[if supportFields]><span
6003 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732187
6004 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6005 style='mso-no-proof:yes'>6<!--[if gte mso 9]><xml>
6006 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100380037000000</w:data>
6007 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6008 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6009 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6010 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6011 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6013 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6014 style='mso-no-proof:yes'>T-Coffee code can be re-used freely<span
6015 style='mso-tab-count:1 dotted'>............................................................................................. </span></span><!--[if supportFields]><span
6016 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732188
6017 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6018 style='mso-no-proof:yes'>6<!--[if gte mso 9]><xml>
6019 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100380038000000</w:data>
6020 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6021 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6022 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6023 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6024 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6026 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6027 style='mso-no-proof:yes'>T-Coffee can be incorporated in most pipelines:
6028 Plug-in/Plug-out
\85<span style='mso-tab-count:1 dotted'>......................................... </span></span><!--[if supportFields]><span
6029 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732189
6030 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6031 style='mso-no-proof:yes'>6<!--[if gte mso 9]><xml>
6032 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100380039000000</w:data>
6033 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6034 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6035 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6036 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6037 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6039 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6040 style='mso-no-proof:yes'>Contributors<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
6041 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732190
6042 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6043 style='mso-no-proof:yes'>7<!--[if gte mso 9]><xml>
6044 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390030000000</w:data>
6045 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6046 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6047 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6048 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6049 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6051 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6052 style='mso-no-proof:yes'>Addresses<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
6053 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732191
6054 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6055 style='mso-no-proof:yes'>7<!--[if gte mso 9]><xml>
6056 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390031000000</w:data>
6057 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6058 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6059 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6060 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6061 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6063 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6064 style='mso-no-proof:yes'>T-Coffee<span style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
6065 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732192
6066 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6067 style='mso-no-proof:yes'>8<!--[if gte mso 9]><xml>
6068 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390032000000</w:data>
6069 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6070 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6071 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6072 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6073 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6075 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6076 style='mso-no-proof:yes'>Mocca<span style='mso-tab-count:1 dotted'>............................................................................................................................................ </span></span><!--[if supportFields]><span
6077 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732193
6078 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6079 style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
6080 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390033000000</w:data>
6081 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6082 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6083 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6084 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6085 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6087 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6088 style='mso-no-proof:yes'>CORE<span style='mso-tab-count:1 dotted'>............................................................................................................................................. </span></span><!--[if supportFields]><span
6089 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732194
6090 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6091 style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
6092 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390034000000</w:data>
6093 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6094 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6095 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6096 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6097 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6099 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6100 style='mso-no-proof:yes'>Other Contributions<span style='mso-tab-count:1 dotted'>.................................................................................................................... </span></span><!--[if supportFields]><span
6101 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732195
6102 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6103 style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
6104 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390035000000</w:data>
6105 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6106 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6107 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6108 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6109 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6111 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6112 style='mso-no-proof:yes'>Bug Reports and Feedback<span style='mso-tab-count:
6113 1 dotted'>......................................................................................................... </span></span><!--[if supportFields]><span
6114 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732196
6115 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6116 style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
6117 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390036000000</w:data>
6118 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6119 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6120 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6121 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6122 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6124 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6125 style='mso-no-proof:yes'>Third Party Packages and On Demand Installations<span
6126 style='mso-tab-count:1 dotted'>................................................................ </span></span><!--[if supportFields]><span
6127 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732197
6128 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6129 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6130 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390037000000</w:data>
6131 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6132 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6133 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6134 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6135 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6137 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6138 style='mso-no-proof:yes'>Standard Installation of T-Coffee<span
6139 style='mso-tab-count:1 dotted'>............................................................................................... </span></span><!--[if supportFields]><span
6140 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732198
6141 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6142 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6143 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390038000000</w:data>
6144 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6145 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6146 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6147 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6148 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6150 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6151 style='mso-hansi-font-family:"Arial Black";mso-no-proof:yes'>Automated
6152 Installation</span><span style='mso-no-proof:yes'><span style='mso-tab-count:
6153 1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6154 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732199
6155 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6156 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6157 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390039000000</w:data>
6158 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6159 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6160 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6161 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6162 mso-no-proof:yes'><o:p></o:p></span></p>
6164 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6165 style='mso-no-proof:yes'>Mac-OsX<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
6166 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732200
6167 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6168 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6169 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300030000000</w:data>
6170 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6171 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6172 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6173 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6174 mso-no-proof:yes'><o:p></o:p></span></p>
6176 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6177 style='mso-no-proof:yes'>Unix<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6178 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732201
6179 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6180 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6181 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300031000000</w:data>
6182 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6183 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6184 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6185 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6186 mso-no-proof:yes'><o:p></o:p></span></p>
6188 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6189 style='mso-hansi-font-family:"Arial Black";mso-no-proof:yes'>Unix</span><span
6190 style='mso-no-proof:yes'><span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6191 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732202
6192 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6193 style='mso-no-proof:yes'>12<!--[if gte mso 9]><xml>
6194 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300032000000</w:data>
6195 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6196 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6197 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6198 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6199 mso-no-proof:yes'><o:p></o:p></span></p>
6201 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6202 style='mso-no-proof:yes'>Microsoft Windows/Cygwin<span style='mso-tab-count:
6203 1 dotted'>............................................................................................................................................................ </span></span><!--[if supportFields]><span
6204 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732203
6205 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6206 style='mso-no-proof:yes'>13<!--[if gte mso 9]><xml>
6207 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300033000000</w:data>
6208 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6209 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6210 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6211 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6212 mso-no-proof:yes'><o:p></o:p></span></p>
6214 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6215 style='mso-no-proof:yes'>MAC osX, Linux<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6216 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732204
6217 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6218 style='mso-no-proof:yes'>13<!--[if gte mso 9]><xml>
6219 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300034000000</w:data>
6220 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6221 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6222 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6223 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6224 mso-no-proof:yes'><o:p></o:p></span></p>
6226 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6227 style='mso-no-proof:yes'>CLUSTER Installation<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................. </span></span><!--[if supportFields]><span
6228 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732205
6229 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6230 style='mso-no-proof:yes'>13<!--[if gte mso 9]><xml>
6231 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300035000000</w:data>
6232 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6233 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6234 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6235 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6236 mso-no-proof:yes'><o:p></o:p></span></p>
6238 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6239 style='mso-no-proof:yes'>If you have PDB installed:<span style='mso-tab-count:
6240 1 dotted'>.................................................................................................................................................................... </span></span><!--[if supportFields]><span
6241 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732206
6242 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6243 style='mso-no-proof:yes'>14<!--[if gte mso 9]><xml>
6244 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300036000000</w:data>
6245 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6246 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6247 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6248 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6249 mso-no-proof:yes'><o:p></o:p></span></p>
6251 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6252 style='mso-no-proof:yes'>Installing BLAST for T-Coffee<span style='mso-tab-count:
6253 1 dotted'>...................................................................................................... </span></span><!--[if supportFields]><span
6254 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732207
6255 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6256 style='mso-no-proof:yes'>14<!--[if gte mso 9]><xml>
6257 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300037000000</w:data>
6258 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6259 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6260 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6261 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6262 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6264 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6265 style='mso-no-proof:yes'>Why Do I need BLAST with T-Coffee?<span
6266 style='mso-tab-count:1 dotted'>......................................................................................................................................... </span></span><!--[if supportFields]><span
6267 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732208
6268 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6269 style='mso-no-proof:yes'>14<!--[if gte mso 9]><xml>
6270 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300038000000</w:data>
6271 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6272 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6273 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6274 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6275 mso-no-proof:yes'><o:p></o:p></span></p>
6277 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6278 style='mso-no-proof:yes'>Using the EBI BLAST Client<span style='mso-tab-count:
6279 1 dotted'>................................................................................................................................................................ </span></span><!--[if supportFields]><span
6280 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732209
6281 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6282 style='mso-no-proof:yes'>15<!--[if gte mso 9]><xml>
6283 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300039000000</w:data>
6284 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6285 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6286 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6287 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6288 mso-no-proof:yes'><o:p></o:p></span></p>
6290 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6291 style='mso-no-proof:yes'>Using the NCBI BLAST Client<span style='mso-tab-count:
6292 1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
6293 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732210
6294 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6295 style='mso-no-proof:yes'>15<!--[if gte mso 9]><xml>
6296 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310030000000</w:data>
6297 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6298 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6299 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6300 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6301 mso-no-proof:yes'><o:p></o:p></span></p>
6303 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6304 style='mso-no-proof:yes'>Using another Client<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
6305 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732211
6306 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6307 style='mso-no-proof:yes'>16<!--[if gte mso 9]><xml>
6308 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310031000000</w:data>
6309 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6310 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6311 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6312 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6313 mso-no-proof:yes'><o:p></o:p></span></p>
6315 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6316 style='mso-no-proof:yes'>Using a BLAST local version on UNIX<span
6317 style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
6318 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732212
6319 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6320 style='mso-no-proof:yes'>16<!--[if gte mso 9]><xml>
6321 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310032000000</w:data>
6322 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6323 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6324 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6325 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6326 mso-no-proof:yes'><o:p></o:p></span></p>
6328 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6329 style='mso-no-proof:yes'>Using a BLAST local version on Windows/cygwin<span
6330 style='mso-tab-count:1 dotted'>............................................................................................................ </span></span><!--[if supportFields]><span
6331 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732213
6332 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6333 style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
6334 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310033000000</w:data>
6335 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6336 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6337 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6338 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6339 mso-no-proof:yes'><o:p></o:p></span></p>
6341 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6342 style='mso-no-proof:yes'>BLAST+<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6343 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732214
6344 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6345 style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
6346 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310034000000</w:data>
6347 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6348 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6349 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6350 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6351 mso-no-proof:yes'><o:p></o:p></span></p>
6353 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6354 style='mso-no-proof:yes'>ORIGINAL NCBI BLAST<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6355 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732215
6356 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6357 style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
6358 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310035000000</w:data>
6359 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6360 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6361 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6362 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6363 mso-no-proof:yes'><o:p></o:p></span></p>
6365 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6366 style='mso-no-proof:yes'>Installing Other Companion Packages<span
6367 style='mso-tab-count:1 dotted'>....................................................................................... </span></span><!--[if supportFields]><span
6368 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732216
6369 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6370 style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
6371 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310036000000</w:data>
6372 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6373 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6374 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6375 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6376 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6378 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6379 style='mso-no-proof:yes'>Installation of PSI-Coffee and Expresso<span
6380 style='mso-tab-count:1 dotted'>..................................................................................... </span></span><!--[if supportFields]><span
6381 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732217
6382 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6383 style='mso-no-proof:yes'>19<!--[if gte mso 9]><xml>
6384 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310037000000</w:data>
6385 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6386 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6387 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6388 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6389 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6391 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6392 style='mso-no-proof:yes'>Installation of M-Coffee<span style='mso-tab-count:
6393 1 dotted'>............................................................................................................... </span></span><!--[if supportFields]><span
6394 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732218
6395 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6396 style='mso-no-proof:yes'>19<!--[if gte mso 9]><xml>
6397 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310038000000</w:data>
6398 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6399 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6400 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6401 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6402 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6404 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6405 style='mso-no-proof:yes'>Automated Installation<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6406 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732219
6407 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6408 style='mso-no-proof:yes'>20<!--[if gte mso 9]><xml>
6409 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310039000000</w:data>
6410 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6411 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6412 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6413 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6414 mso-no-proof:yes'><o:p></o:p></span></p>
6416 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6417 style='mso-no-proof:yes'>Manual Installation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6418 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732220
6419 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6420 style='mso-no-proof:yes'>20<!--[if gte mso 9]><xml>
6421 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320030000000</w:data>
6422 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6423 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6424 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6425 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6426 mso-no-proof:yes'><o:p></o:p></span></p>
6428 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6429 style='mso-no-proof:yes'>Installation of APDB and iRMSD<span style='mso-tab-count:
6430 1 dotted'>.................................................................................................. </span></span><!--[if supportFields]><span
6431 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732221
6432 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6433 style='mso-no-proof:yes'>22<!--[if gte mso 9]><xml>
6434 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320031000000</w:data>
6435 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6436 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6437 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6438 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6439 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6441 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6442 style='mso-no-proof:yes'>Installation of tRMSD<span style='mso-tab-count:1 dotted'>................................................................................................................... </span></span><!--[if supportFields]><span
6443 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732222
6444 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6445 style='mso-no-proof:yes'>22<!--[if gte mso 9]><xml>
6446 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320032000000</w:data>
6447 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6448 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6449 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6450 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6451 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6453 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6454 style='mso-no-proof:yes'>Installation of seq_reformat<span style='mso-tab-count:
6455 1 dotted'>........................................................................................................ </span></span><!--[if supportFields]><span
6456 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732223
6457 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6458 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6459 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320033000000</w:data>
6460 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6461 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6462 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6463 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6464 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6466 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6467 style='mso-no-proof:yes'>Installation of extract_from_pdb<span
6468 style='mso-tab-count:1 dotted'>................................................................................................ </span></span><!--[if supportFields]><span
6469 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732224
6470 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6471 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6472 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320034000000</w:data>
6473 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6474 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6475 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6476 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6477 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6479 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6480 style='mso-no-proof:yes'>Installation of 3D-Coffee/Expresso<span
6481 style='mso-tab-count:1 dotted'>............................................................................................ </span></span><!--[if supportFields]><span
6482 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732225
6483 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6484 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6485 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320035000000</w:data>
6486 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6487 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6488 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6489 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6490 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6492 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6493 style='mso-no-proof:yes'>Automated Installation<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6494 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732226
6495 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6496 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6497 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320036000000</w:data>
6498 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6499 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6500 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6501 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6502 mso-no-proof:yes'><o:p></o:p></span></p>
6504 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6505 style='mso-no-proof:yes'>Manual Installation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6506 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732227
6507 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6508 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6509 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320037000000</w:data>
6510 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6511 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6512 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6513 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6514 mso-no-proof:yes'><o:p></o:p></span></p>
6516 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6517 style='mso-no-proof:yes'>Installing Fugue for T-Coffee<span style='mso-tab-count:
6518 1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
6519 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732228
6520 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6521 style='mso-no-proof:yes'>24<!--[if gte mso 9]><xml>
6522 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320038000000</w:data>
6523 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6524 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6525 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6526 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6527 mso-no-proof:yes'><o:p></o:p></span></p>
6529 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6530 style='mso-no-proof:yes'>Installation of R-Coffee<span style='mso-tab-count:
6531 1 dotted'>................................................................................................................ </span></span><!--[if supportFields]><span
6532 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732229
6533 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6534 style='mso-no-proof:yes'>24<!--[if gte mso 9]><xml>
6535 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320039000000</w:data>
6536 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6537 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6538 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6539 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6540 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6542 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6543 style='mso-no-proof:yes'>Automated Installation<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6544 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732230
6545 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6546 style='mso-no-proof:yes'>24<!--[if gte mso 9]><xml>
6547 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330030000000</w:data>
6548 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6549 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6550 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6551 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6552 mso-no-proof:yes'><o:p></o:p></span></p>
6554 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6555 style='mso-no-proof:yes'>Manual Installation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6556 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732231
6557 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6558 style='mso-no-proof:yes'>25<!--[if gte mso 9]><xml>
6559 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330031000000</w:data>
6560 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6561 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6562 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6563 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6564 mso-no-proof:yes'><o:p></o:p></span></p>
6566 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6567 style='mso-no-proof:yes'>Installing ProbbonsRNA for R-Coffee<span
6568 style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
6569 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732232
6570 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6571 style='mso-no-proof:yes'>25<!--[if gte mso 9]><xml>
6572 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330032000000</w:data>
6573 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6574 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6575 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6576 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6577 mso-no-proof:yes'><o:p></o:p></span></p>
6579 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6580 style='mso-no-proof:yes'>Installing Consan for R-Coffee<span style='mso-tab-count:
6581 1 dotted'>.......................................................................................................................................................... </span></span><!--[if supportFields]><span
6582 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732233
6583 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6584 style='mso-no-proof:yes'>25<!--[if gte mso 9]><xml>
6585 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330033000000</w:data>
6586 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6587 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6588 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6589 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6590 mso-no-proof:yes'><o:p></o:p></span></p>
6592 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6593 style='mso-no-proof:yes'>T-COFFEE<span style='mso-tab-count:1 dotted'>...................................................................................................................................... </span></span><!--[if supportFields]><span
6594 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732234
6595 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6596 style='mso-no-proof:yes'>26<!--[if gte mso 9]><xml>
6597 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330034000000</w:data>
6598 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6599 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6600 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6601 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6602 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6604 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6605 style='mso-no-proof:yes'>M-Coffee<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
6606 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732235
6607 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6608 style='mso-no-proof:yes'>26<!--[if gte mso 9]><xml>
6609 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330035000000</w:data>
6610 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6611 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6612 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6613 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6614 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6616 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6617 style='mso-no-proof:yes'>Expresso<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
6618 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732236
6619 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6620 style='mso-no-proof:yes'>27<!--[if gte mso 9]><xml>
6621 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330036000000</w:data>
6622 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6623 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6624 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6625 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6626 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6628 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6629 style='mso-no-proof:yes'>R-Coffee<span style='mso-tab-count:1 dotted'>........................................................................................................................................ </span></span><!--[if supportFields]><span
6630 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732237
6631 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6632 style='mso-no-proof:yes'>27<!--[if gte mso 9]><xml>
6633 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330037000000</w:data>
6634 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6635 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6636 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6637 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6638 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6640 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6641 style='mso-no-proof:yes'>iRMSD and APDB<span style='mso-tab-count:1 dotted'>.......................................................................................................................... </span></span><!--[if supportFields]><span
6642 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732238
6643 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6644 style='mso-no-proof:yes'>28<!--[if gte mso 9]><xml>
6645 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330038000000</w:data>
6646 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6647 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6648 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6649 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6650 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6652 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6653 style='mso-no-proof:yes'>tRMSD<span style='mso-tab-count:1 dotted'>........................................................................................................................................... </span></span><!--[if supportFields]><span
6654 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732239
6655 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6656 style='mso-no-proof:yes'>28<!--[if gte mso 9]><xml>
6657 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330039000000</w:data>
6658 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6659 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6660 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6661 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6662 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6664 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6665 style='mso-no-proof:yes'>MOCCA<span style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
6666 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732240
6667 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6668 style='mso-no-proof:yes'>29<!--[if gte mso 9]><xml>
6669 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340030000000</w:data>
6670 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6671 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6672 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6673 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6674 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6676 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6677 style='mso-no-proof:yes'>Environment Variables<span style='mso-tab-count:1 dotted'>............................................................................................................... </span></span><!--[if supportFields]><span
6678 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732241
6679 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6680 style='mso-no-proof:yes'>31<!--[if gte mso 9]><xml>
6681 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340031000000</w:data>
6682 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6683 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6684 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6685 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6686 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6688 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6689 style='mso-no-proof:yes'>http_proxy_4_TCOFFEE<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................ </span></span><!--[if supportFields]><span
6690 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732242
6691 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6692 style='mso-no-proof:yes'>31<!--[if gte mso 9]><xml>
6693 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340032000000</w:data>
6694 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6695 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6696 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6697 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6698 mso-no-proof:yes'><o:p></o:p></span></p>
6700 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6701 style='mso-no-proof:yes'>email_4_TCOFFEE<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6702 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732243
6703 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6704 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6705 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340033000000</w:data>
6706 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6707 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6708 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6709 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6710 mso-no-proof:yes'><o:p></o:p></span></p>
6712 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6713 style='mso-no-proof:yes'>DIR_4_TCOFFEE<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6714 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732244
6715 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6716 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6717 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340034000000</w:data>
6718 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6719 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6720 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6721 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6722 mso-no-proof:yes'><o:p></o:p></span></p>
6724 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6725 style='mso-no-proof:yes'>TMP_4_TCOFFEE<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6726 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732245
6727 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6728 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6729 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340035000000</w:data>
6730 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6731 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6732 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6733 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6734 mso-no-proof:yes'><o:p></o:p></span></p>
6736 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6737 style='mso-no-proof:yes'>CACHE_4_TCOFFEE<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6738 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732246
6739 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6740 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6741 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340036000000</w:data>
6742 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6743 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6744 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6745 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6746 mso-no-proof:yes'><o:p></o:p></span></p>
6748 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6749 style='mso-no-proof:yes'>PLUGINS_4_TCOFFEE<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................. </span></span><!--[if supportFields]><span
6750 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732247
6751 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6752 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6753 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340037000000</w:data>
6754 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6755 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6756 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6757 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6758 mso-no-proof:yes'><o:p></o:p></span></p>
6760 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6761 style='mso-no-proof:yes'>NO_ERROR_REPORT_4_TCOFFEE<span style='mso-tab-count:
6762 1 dotted'>.................................................................................................................................................. </span></span><!--[if supportFields]><span
6763 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732248
6764 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6765 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6766 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340038000000</w:data>
6767 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6768 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6769 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6770 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6771 mso-no-proof:yes'><o:p></o:p></span></p>
6773 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6774 style='mso-no-proof:yes'>PDB_DIR<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6775 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732249
6776 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6777 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6778 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340039000000</w:data>
6779 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6780 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6781 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6782 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6783 mso-no-proof:yes'><o:p></o:p></span></p>
6785 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6786 style='mso-no-proof:yes'>NO_WARNING_4_TCOFFEE<span style='mso-tab-count:1 dotted'>................................................................................................................................................................ </span></span><!--[if supportFields]><span
6787 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732250
6788 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6789 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6790 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350030000000</w:data>
6791 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6792 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6793 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6794 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6795 mso-no-proof:yes'><o:p></o:p></span></p>
6797 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6798 style='mso-no-proof:yes'>UNIQUE_DIR_4_TCOFFEE<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................... </span></span><!--[if supportFields]><span
6799 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732251
6800 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6801 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6802 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350031000000</w:data>
6803 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6804 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6805 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6806 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6807 mso-no-proof:yes'><o:p></o:p></span></p>
6809 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6810 style='mso-no-proof:yes'>Setting up the T-Coffee environment variables<span
6811 style='mso-tab-count:1 dotted'>........................................................................ </span></span><!--[if supportFields]><span
6812 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732252
6813 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6814 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6815 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350032000000</w:data>
6816 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6817 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6818 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6819 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6820 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6822 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6823 style='mso-no-proof:yes'>Well Behaved Parameters<span style='mso-tab-count:
6824 1 dotted'>.......................................................................................................... </span></span><!--[if supportFields]><span
6825 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732253
6826 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6827 style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
6828 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350033000000</w:data>
6829 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6830 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6831 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6832 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6833 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6835 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6836 style='mso-no-proof:yes'>Separation<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6837 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732254
6838 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6839 style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
6840 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350034000000</w:data>
6841 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6842 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6843 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6844 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6845 mso-no-proof:yes'><o:p></o:p></span></p>
6847 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6848 style='mso-no-proof:yes'>Posix<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6849 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732255
6850 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6851 style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
6852 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350035000000</w:data>
6853 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6854 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6855 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6856 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6857 mso-no-proof:yes'><o:p></o:p></span></p>
6859 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6860 style='mso-no-proof:yes'>Entering the right parameters<span style='mso-tab-count:
6861 1 dotted'>.......................................................................................................................................................... </span></span><!--[if supportFields]><span
6862 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732256
6863 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6864 style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
6865 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350036000000</w:data>
6866 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6867 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6868 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6869 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6870 mso-no-proof:yes'><o:p></o:p></span></p>
6872 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6873 style='mso-no-proof:yes'>Parameters Syntax<span style='mso-tab-count:1 dotted'>...................................................................................................................... </span></span><!--[if supportFields]><span
6874 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732257
6875 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6876 style='mso-no-proof:yes'>34<!--[if gte mso 9]><xml>
6877 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350037000000</w:data>
6878 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6879 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6880 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6881 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6882 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6884 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6885 style='mso-no-proof:yes'>No Flag<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6886 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732258
6887 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6888 style='mso-no-proof:yes'>34<!--[if gte mso 9]><xml>
6889 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350038000000</w:data>
6890 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6891 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6892 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6893 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6894 mso-no-proof:yes'><o:p></o:p></span></p>
6896 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6897 style='mso-no-proof:yes'>-parameters<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6898 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732259
6899 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6900 style='mso-no-proof:yes'>34<!--[if gte mso 9]><xml>
6901 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350039000000</w:data>
6902 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6903 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6904 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6905 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6906 mso-no-proof:yes'><o:p></o:p></span></p>
6908 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6909 style='mso-no-proof:yes'>-t_coffee_defaults<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6910 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732260
6911 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6912 style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
6913 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360030000000</w:data>
6914 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6915 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6916 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6917 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6918 mso-no-proof:yes'><o:p></o:p></span></p>
6920 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6921 style='mso-no-proof:yes'>-mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6922 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732261
6923 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6924 style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
6925 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360031000000</w:data>
6926 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6927 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6928 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6929 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6930 mso-no-proof:yes'><o:p></o:p></span></p>
6932 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6933 style='mso-no-proof:yes'>-score [Deprecated]<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
6934 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732262
6935 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6936 style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
6937 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360032000000</w:data>
6938 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6939 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6940 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6941 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6942 mso-no-proof:yes'><o:p></o:p></span></p>
6944 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6945 style='mso-no-proof:yes'>-evaluate<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6946 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732263
6947 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6948 style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
6949 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360033000000</w:data>
6950 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6951 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6952 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6953 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6954 mso-no-proof:yes'><o:p></o:p></span></p>
6956 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6957 style='mso-no-proof:yes'>-convert [cw]<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6958 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732264
6959 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6960 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
6961 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360034000000</w:data>
6962 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6963 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6964 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6965 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6966 mso-no-proof:yes'><o:p></o:p></span></p>
6968 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6969 style='mso-no-proof:yes'>-do_align [cw]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
6970 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732265
6971 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6972 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
6973 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360035000000</w:data>
6974 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6975 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6976 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6977 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6978 mso-no-proof:yes'><o:p></o:p></span></p>
6980 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6981 style='mso-no-proof:yes'>Special Parameters<span style='mso-tab-count:1 dotted'>...................................................................................................................... </span></span><!--[if supportFields]><span
6982 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732266
6983 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6984 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
6985 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360036000000</w:data>
6986 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6987 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6988 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6989 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6990 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6992 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6993 style='mso-no-proof:yes'>-version<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6994 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732267
6995 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6996 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
6997 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360037000000</w:data>
6998 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6999 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7000 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7001 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7002 mso-no-proof:yes'><o:p></o:p></span></p>
7004 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7005 style='mso-no-proof:yes'>-proxy<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7006 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732268
7007 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7008 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
7009 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360038000000</w:data>
7010 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7011 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7012 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7013 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7014 mso-no-proof:yes'><o:p></o:p></span></p>
7016 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7017 style='mso-no-proof:yes'>-email<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7018 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732269
7019 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7020 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
7021 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360039000000</w:data>
7022 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7023 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7024 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7025 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7026 mso-no-proof:yes'><o:p></o:p></span></p>
7028 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7029 style='mso-no-proof:yes'>-check_configuration<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................. </span></span><!--[if supportFields]><span
7030 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732270
7031 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7032 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7033 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370030000000</w:data>
7034 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7035 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7036 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7037 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7038 mso-no-proof:yes'><o:p></o:p></span></p>
7040 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7041 style='mso-no-proof:yes'>-cache<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7042 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732271
7043 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7044 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7045 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370031000000</w:data>
7046 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7047 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7048 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7049 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7050 mso-no-proof:yes'><o:p></o:p></span></p>
7052 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7053 style='mso-no-proof:yes'>-update<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7054 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732272
7055 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7056 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7057 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370032000000</w:data>
7058 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7059 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7060 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7061 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7062 mso-no-proof:yes'><o:p></o:p></span></p>
7064 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7065 style='mso-no-proof:yes'>-full_log<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7066 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732273
7067 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7068 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7069 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370033000000</w:data>
7070 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7071 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7072 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7073 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7074 mso-no-proof:yes'><o:p></o:p></span></p>
7076 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7077 style='mso-no-proof:yes'>-plugins<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7078 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732274
7079 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7080 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7081 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370034000000</w:data>
7082 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7083 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7084 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7085 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7086 mso-no-proof:yes'><o:p></o:p></span></p>
7088 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7089 style='mso-no-proof:yes'>-other_pg<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7090 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732275
7091 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7092 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7093 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370035000000</w:data>
7094 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7095 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7096 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7097 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7098 mso-no-proof:yes'><o:p></o:p></span></p>
7100 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
7101 style='mso-no-proof:yes'>Input<span style='mso-tab-count:1 dotted'>............................................................................................................................................. </span></span><!--[if supportFields]><span
7102 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732276
7103 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7104 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7105 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370036000000</w:data>
7106 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7107 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7108 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7109 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7110 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
7112 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7113 style='mso-no-proof:yes'>Sequence Input<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7114 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732277
7115 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7116 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7117 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370037000000</w:data>
7118 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7119 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7120 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7121 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7122 mso-no-proof:yes'><o:p></o:p></span></p>
7124 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7125 style='mso-no-proof:yes'>-infile [cw]<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7126 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732278
7127 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7128 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7129 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370038000000</w:data>
7130 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7131 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7132 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7133 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7134 mso-no-proof:yes'><o:p></o:p></span></p>
7136 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7137 style='mso-no-proof:yes'>-in (Cf –in from the Method and Library Input
7138 section)<span style='mso-tab-count:1 dotted'>........................................................................................................ </span></span><!--[if supportFields]><span
7139 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732279
7140 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7141 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7142 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370039000000</w:data>
7143 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7144 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7145 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7146 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7147 mso-no-proof:yes'><o:p></o:p></span></p>
7149 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7150 style='mso-no-proof:yes'>-get_type<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7151 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732280
7152 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7153 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7154 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380030000000</w:data>
7155 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7156 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7157 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7158 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7159 mso-no-proof:yes'><o:p></o:p></span></p>
7161 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7162 style='mso-no-proof:yes'>-type [cw]<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7163 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732281
7164 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7165 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7166 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380031000000</w:data>
7167 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7168 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7169 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7170 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7171 mso-no-proof:yes'><o:p></o:p></span></p>
7173 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7174 style='mso-no-proof:yes'>-seq<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7175 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732282
7176 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7177 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7178 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380032000000</w:data>
7179 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7180 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7181 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7182 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7183 mso-no-proof:yes'><o:p></o:p></span></p>
7185 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7186 style='mso-no-proof:yes'>-seq_source<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7187 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732283
7188 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7189 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7190 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380033000000</w:data>
7191 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7192 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7193 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7194 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7195 mso-no-proof:yes'><o:p></o:p></span></p>
7197 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7198 style='mso-no-proof:yes'>Structure Input<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7199 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732284
7200 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7201 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7202 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380034000000</w:data>
7203 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7204 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7205 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7206 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7207 mso-no-proof:yes'><o:p></o:p></span></p>
7209 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7210 style='mso-no-proof:yes'>-pdb<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7211 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732285
7212 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7213 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7214 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380035000000</w:data>
7215 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7216 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7217 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7218 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7219 mso-no-proof:yes'><o:p></o:p></span></p>
7221 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7222 style='mso-no-proof:yes'>Tree Input<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7223 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732286
7224 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7225 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7226 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380036000000</w:data>
7227 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7228 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7229 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7230 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7231 mso-no-proof:yes'><o:p></o:p></span></p>
7233 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7234 style='mso-no-proof:yes'>-usetree<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7235 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732287
7236 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7237 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7238 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380037000000</w:data>
7239 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7240 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7241 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7242 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7243 mso-no-proof:yes'><o:p></o:p></span></p>
7245 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7246 style='mso-no-proof:yes'>Structures, Sequences Methods and Library Input via
7247 the -in Flag<span style='mso-tab-count:1 dotted'>......................................................................... </span></span><!--[if supportFields]><span
7248 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732288
7249 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7250 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7251 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380038000000</w:data>
7252 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7253 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7254 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7255 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7256 mso-no-proof:yes'><o:p></o:p></span></p>
7258 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7259 style='mso-no-proof:yes'>-in<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7260 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732289
7261 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7262 style='mso-no-proof:yes'>40<!--[if gte mso 9]><xml>
7263 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380039000000</w:data>
7264 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7265 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7266 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7267 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7268 mso-no-proof:yes'><o:p></o:p></span></p>
7270 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7271 style='mso-no-proof:yes'>Profile Input<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7272 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732290
7273 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7274 style='mso-no-proof:yes'>41<!--[if gte mso 9]><xml>
7275 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390030000000</w:data>
7276 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7277 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7278 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7279 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7280 mso-no-proof:yes'><o:p></o:p></span></p>
7282 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7283 style='mso-no-proof:yes'>-profile<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7284 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732291
7285 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7286 style='mso-no-proof:yes'>41<!--[if gte mso 9]><xml>
7287 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390031000000</w:data>
7288 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7289 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7290 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7291 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7292 mso-no-proof:yes'><o:p></o:p></span></p>
7294 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7295 style='mso-no-proof:yes'>-profile1 [cw]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7296 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732292
7297 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7298 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7299 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390032000000</w:data>
7300 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7301 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7302 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7303 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7304 mso-no-proof:yes'><o:p></o:p></span></p>
7306 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7307 style='mso-no-proof:yes'>-profile2 [cw]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7308 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732293
7309 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7310 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7311 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390033000000</w:data>
7312 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7313 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7314 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7315 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7316 mso-no-proof:yes'><o:p></o:p></span></p>
7318 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
7319 style='mso-no-proof:yes'>Alignment Computation<span style='mso-tab-count:1 dotted'>.............................................................................................................. </span></span><!--[if supportFields]><span
7320 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732294
7321 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7322 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7323 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390034000000</w:data>
7324 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7325 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7326 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7327 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7328 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
7330 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7331 style='mso-no-proof:yes'>Library Computation: Methods<span style='mso-tab-count:
7332 1 dotted'>...................................................................................................................................................... </span></span><!--[if supportFields]><span
7333 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732295
7334 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7335 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7336 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390035000000</w:data>
7337 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7338 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7339 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7340 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7341 mso-no-proof:yes'><o:p></o:p></span></p>
7343 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7344 style='mso-no-proof:yes'>-lalign_n_top<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7345 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732296
7346 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7347 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7348 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390036000000</w:data>
7349 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7350 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7351 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7352 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7353 mso-no-proof:yes'><o:p></o:p></span></p>
7355 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7356 style='mso-no-proof:yes'>-align_pdb_param_file<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................... </span></span><!--[if supportFields]><span
7357 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732297
7358 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7359 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7360 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390037000000</w:data>
7361 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7362 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7363 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7364 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7365 mso-no-proof:yes'><o:p></o:p></span></p>
7367 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7368 style='mso-no-proof:yes'>-align_pdb_hasch_mode<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................... </span></span><!--[if supportFields]><span
7369 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732298
7370 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7371 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7372 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390038000000</w:data>
7373 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7374 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7375 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7376 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7377 mso-no-proof:yes'><o:p></o:p></span></p>
7379 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7380 style='mso-no-proof:yes'>Library Computation: Extension<span style='mso-tab-count:
7381 1 dotted'>.................................................................................................................................................... </span></span><!--[if supportFields]><span
7382 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732299
7383 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7384 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7385 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390039000000</w:data>
7386 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7387 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7388 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7389 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7390 mso-no-proof:yes'><o:p></o:p></span></p>
7392 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7393 style='mso-no-proof:yes'>-lib_list [Unsupported]<span style='mso-tab-count:
7394 1 dotted'>.......................................................................................................................................................................... </span></span><!--[if supportFields]><span
7395 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732300
7396 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7397 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7398 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300030000000</w:data>
7399 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7400 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7401 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7402 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7403 mso-no-proof:yes'><o:p></o:p></span></p>
7405 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7406 style='mso-no-proof:yes'>-do_normalise<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7407 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732301
7408 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7409 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7410 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300031000000</w:data>
7411 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7412 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7413 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7414 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7415 mso-no-proof:yes'><o:p></o:p></span></p>
7417 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7418 style='mso-no-proof:yes'>-extend<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7419 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732302
7420 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7421 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7422 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300032000000</w:data>
7423 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7424 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7425 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7426 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7427 mso-no-proof:yes'><o:p></o:p></span></p>
7429 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7430 style='mso-no-proof:yes'>-extend_mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7431 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732303
7432 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7433 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7434 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300033000000</w:data>
7435 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7436 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7437 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7438 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7439 mso-no-proof:yes'><o:p></o:p></span></p>
7441 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7442 style='mso-no-proof:yes'>-max_n_pair<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7443 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732304
7444 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7445 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7446 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300034000000</w:data>
7447 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7448 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7449 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7450 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7451 mso-no-proof:yes'><o:p></o:p></span></p>
7453 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7454 style='mso-no-proof:yes'>-seq_name_for_quadruplet<span style='mso-tab-count:
7455 1 dotted'>.................................................................................................................................................................. </span></span><!--[if supportFields]><span
7456 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732305
7457 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7458 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7459 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300035000000</w:data>
7460 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7461 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7462 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7463 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7464 mso-no-proof:yes'><o:p></o:p></span></p>
7466 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7467 style='mso-no-proof:yes'>-compact<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7468 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732306
7469 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7470 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7471 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300036000000</w:data>
7472 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7473 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7474 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7475 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7476 mso-no-proof:yes'><o:p></o:p></span></p>
7478 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7479 style='mso-no-proof:yes'>-clean<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7480 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732307
7481 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7482 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7483 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300037000000</w:data>
7484 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7485 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7486 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7487 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7488 mso-no-proof:yes'><o:p></o:p></span></p>
7490 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7491 style='mso-no-proof:yes'>-maximise<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7492 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732308
7493 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7494 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7495 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300038000000</w:data>
7496 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7497 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7498 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7499 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7500 mso-no-proof:yes'><o:p></o:p></span></p>
7502 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7503 style='mso-no-proof:yes'>-do_self<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7504 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732309
7505 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7506 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7507 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300039000000</w:data>
7508 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7509 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7510 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7511 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7512 mso-no-proof:yes'><o:p></o:p></span></p>
7514 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7515 style='mso-no-proof:yes'>-seq_name_for_quadruplet<span style='mso-tab-count:
7516 1 dotted'>.................................................................................................................................................................. </span></span><!--[if supportFields]><span
7517 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732310
7518 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7519 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7520 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310030000000</w:data>
7521 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7522 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7523 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7524 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7525 mso-no-proof:yes'><o:p></o:p></span></p>
7527 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7528 style='mso-no-proof:yes'>-weight<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7529 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732311
7530 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7531 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7532 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310031000000</w:data>
7533 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7534 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7535 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7536 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7537 mso-no-proof:yes'><o:p></o:p></span></p>
7539 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7540 style='mso-no-proof:yes'>Tree Computation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7541 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732312
7542 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7543 style='mso-no-proof:yes'>45<!--[if gte mso 9]><xml>
7544 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310032000000</w:data>
7545 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7546 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7547 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7548 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7549 mso-no-proof:yes'><o:p></o:p></span></p>
7551 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7552 style='mso-no-proof:yes'>-distance_matrix_mode<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
7553 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732313
7554 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7555 style='mso-no-proof:yes'>45<!--[if gte mso 9]><xml>
7556 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310033000000</w:data>
7557 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7558 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7559 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7560 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7561 mso-no-proof:yes'><o:p></o:p></span></p>
7563 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7564 style='mso-no-proof:yes'>-quicktree [CW]<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7565 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732314
7566 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7567 style='mso-no-proof:yes'>45<!--[if gte mso 9]><xml>
7568 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310034000000</w:data>
7569 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7570 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7571 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7572 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7573 mso-no-proof:yes'><o:p></o:p></span></p>
7575 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7576 style='mso-no-proof:yes'>Pair-wise Alignment Computation<span style='mso-tab-count:
7577 1 dotted'>................................................................................................................................................ </span></span><!--[if supportFields]><span
7578 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732315
7579 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7580 style='mso-no-proof:yes'>46<!--[if gte mso 9]><xml>
7581 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310035000000</w:data>
7582 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7583 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7584 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7585 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7586 mso-no-proof:yes'><o:p></o:p></span></p>
7588 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7589 style='mso-no-proof:yes'>-dp_mode<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7590 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732316
7591 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7592 style='mso-no-proof:yes'>46<!--[if gte mso 9]><xml>
7593 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310036000000</w:data>
7594 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7595 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7596 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7597 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7598 mso-no-proof:yes'><o:p></o:p></span></p>
7600 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7601 style='mso-no-proof:yes'>-ktuple<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7602 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732317
7603 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7604 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7605 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310037000000</w:data>
7606 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7607 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7608 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7609 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7610 mso-no-proof:yes'><o:p></o:p></span></p>
7612 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7613 style='mso-no-proof:yes'>-ndiag<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7614 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732318
7615 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7616 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7617 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310038000000</w:data>
7618 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7619 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7620 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7621 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7622 mso-no-proof:yes'><o:p></o:p></span></p>
7624 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7625 style='mso-no-proof:yes'>-diag_mode<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7626 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732319
7627 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7628 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7629 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310039000000</w:data>
7630 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7631 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7632 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7633 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7634 mso-no-proof:yes'><o:p></o:p></span></p>
7636 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7637 style='mso-no-proof:yes'>-diag_threshold<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7638 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732320
7639 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7640 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7641 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320030000000</w:data>
7642 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7643 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7644 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7645 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7646 mso-no-proof:yes'><o:p></o:p></span></p>
7648 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7649 style='mso-no-proof:yes'>-sim_matrix<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7650 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732321
7651 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7652 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7653 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320031000000</w:data>
7654 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7655 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7656 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7657 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7658 mso-no-proof:yes'><o:p></o:p></span></p>
7660 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7661 style='mso-no-proof:yes'>-matrix [CW]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7662 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732322
7663 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7664 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7665 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320032000000</w:data>
7666 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7667 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7668 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7669 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7670 mso-no-proof:yes'><o:p></o:p></span></p>
7672 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7673 style='mso-no-proof:yes'>-nomatch<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7674 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732323
7675 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7676 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7677 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320033000000</w:data>
7678 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7679 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7680 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7681 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7682 mso-no-proof:yes'><o:p></o:p></span></p>
7684 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7685 style='mso-no-proof:yes'>-gapopen<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7686 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732324
7687 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7688 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7689 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320034000000</w:data>
7690 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7691 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7692 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7693 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7694 mso-no-proof:yes'><o:p></o:p></span></p>
7696 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7697 style='mso-no-proof:yes'>-gapext<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7698 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732325
7699 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7700 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7701 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320035000000</w:data>
7702 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7703 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7704 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7705 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7706 mso-no-proof:yes'><o:p></o:p></span></p>
7708 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7709 style='mso-no-proof:yes'>-fgapopen<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7710 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732326
7711 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7712 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7713 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320036000000</w:data>
7714 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7715 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7716 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7717 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7718 mso-no-proof:yes'><o:p></o:p></span></p>
7720 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7721 style='mso-no-proof:yes'>-fgapext<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7722 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732327
7723 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7724 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7725 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320037000000</w:data>
7726 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7727 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7728 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7729 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7730 mso-no-proof:yes'><o:p></o:p></span></p>
7732 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7733 style='mso-no-proof:yes'>-cosmetic_penalty<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7734 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732328
7735 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7736 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7737 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320038000000</w:data>
7738 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7739 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7740 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7741 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7742 mso-no-proof:yes'><o:p></o:p></span></p>
7744 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7745 style='mso-no-proof:yes'>-tg_mode<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7746 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732329
7747 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7748 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7749 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320039000000</w:data>
7750 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7751 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7752 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7753 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7754 mso-no-proof:yes'><o:p></o:p></span></p>
7756 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7757 style='mso-no-proof:yes'>Weighting Schemes<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7758 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732330
7759 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7760 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7761 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330030000000</w:data>
7762 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7763 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7764 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7765 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7766 mso-no-proof:yes'><o:p></o:p></span></p>
7768 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7769 style='mso-no-proof:yes'>-seq_weight<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7770 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732331
7771 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7772 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7773 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330031000000</w:data>
7774 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7775 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7776 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7777 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7778 mso-no-proof:yes'><o:p></o:p></span></p>
7780 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7781 style='mso-no-proof:yes'>Multiple Alignment Computation<span style='mso-tab-count:
7782 1 dotted'>................................................................................................................................................... </span></span><!--[if supportFields]><span
7783 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732332
7784 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7785 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7786 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330032000000</w:data>
7787 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7788 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7789 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7790 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7791 mso-no-proof:yes'><o:p></o:p></span></p>
7793 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7794 style='mso-no-proof:yes'>-msa_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7795 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732333
7796 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7797 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7798 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330033000000</w:data>
7799 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7800 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7801 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7802 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7803 mso-no-proof:yes'><o:p></o:p></span></p>
7805 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7806 style='mso-no-proof:yes'>-one2all<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7807 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732334
7808 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7809 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7810 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330034000000</w:data>
7811 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7812 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7813 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7814 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7815 mso-no-proof:yes'><o:p></o:p></span></p>
7817 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7818 style='mso-no-proof:yes'>-profile_comparison<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7819 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732335
7820 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7821 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7822 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330035000000</w:data>
7823 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7824 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7825 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7826 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7827 mso-no-proof:yes'><o:p></o:p></span></p>
7829 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7830 style='mso-no-proof:yes'>-profile_mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7831 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732336
7832 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7833 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7834 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330036000000</w:data>
7835 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7836 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7837 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7838 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7839 mso-no-proof:yes'><o:p></o:p></span></p>
7841 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7842 style='mso-no-proof:yes'>Alignment Post-Processing<span style='mso-tab-count:
7843 1 dotted'>................................................................................................................................................................ </span></span><!--[if supportFields]><span
7844 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732337
7845 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7846 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7847 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330037000000</w:data>
7848 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7849 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7850 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7851 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7852 mso-no-proof:yes'><o:p></o:p></span></p>
7854 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7855 style='mso-no-proof:yes'>-clean_aln<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7856 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732338
7857 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7858 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7859 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330038000000</w:data>
7860 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7861 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7862 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7863 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7864 mso-no-proof:yes'><o:p></o:p></span></p>
7866 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7867 style='mso-no-proof:yes'>-clean_threshold<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7868 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732339
7869 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7870 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7871 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330039000000</w:data>
7872 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7873 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7874 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7875 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7876 mso-no-proof:yes'><o:p></o:p></span></p>
7878 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7879 style='mso-no-proof:yes'>-clean_iteration<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7880 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732340
7881 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7882 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7883 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340030000000</w:data>
7884 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7885 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7886 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7887 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7888 mso-no-proof:yes'><o:p></o:p></span></p>
7890 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7891 style='mso-no-proof:yes'>-clean_evaluation_mode<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................... </span></span><!--[if supportFields]><span
7892 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732341
7893 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7894 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7895 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340031000000</w:data>
7896 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7897 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7898 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7899 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7900 mso-no-proof:yes'><o:p></o:p></span></p>
7902 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7903 style='mso-no-proof:yes'>-iterate<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7904 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732342
7905 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7906 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7907 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340032000000</w:data>
7908 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7909 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7910 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7911 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7912 mso-no-proof:yes'><o:p></o:p></span></p>
7914 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
7915 style='mso-no-proof:yes'>BLAST Template Selection Parameters<span
7916 style='mso-tab-count:1 dotted'>...................................................................................... </span></span><!--[if supportFields]><span
7917 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732343
7918 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7919 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7920 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340033000000</w:data>
7921 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7922 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7923 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7924 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7925 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
7927 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7928 style='mso-no-proof:yes'>-blast_server<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7929 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732344
7930 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7931 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7932 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340034000000</w:data>
7933 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7934 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7935 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7936 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7937 mso-no-proof:yes'><o:p></o:p></span></p>
7939 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7940 style='mso-no-proof:yes'>-prot_min_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7941 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732345
7942 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7943 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7944 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340035000000</w:data>
7945 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7946 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7947 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7948 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7949 mso-no-proof:yes'><o:p></o:p></span></p>
7951 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7952 style='mso-no-proof:yes'>-prot_max_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7953 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732346
7954 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7955 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7956 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340036000000</w:data>
7957 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7958 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7959 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7960 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7961 mso-no-proof:yes'><o:p></o:p></span></p>
7963 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7964 style='mso-no-proof:yes'>-prot_min_cov<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7965 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732347
7966 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7967 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7968 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340037000000</w:data>
7969 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7970 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7971 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7972 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7973 mso-no-proof:yes'><o:p></o:p></span></p>
7975 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7976 style='mso-no-proof:yes'>-protein_db<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7977 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732348
7978 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7979 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7980 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340038000000</w:data>
7981 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7982 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7983 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7984 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7985 mso-no-proof:yes'><o:p></o:p></span></p>
7987 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7988 style='mso-no-proof:yes'>-pdb_min_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7989 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732349
7990 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7991 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7992 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340039000000</w:data>
7993 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7994 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7995 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7996 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7997 mso-no-proof:yes'><o:p></o:p></span></p>
7999 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8000 style='mso-no-proof:yes'>-pdb_max_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8001 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732350
8002 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8003 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
8004 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350030000000</w:data>
8005 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8006 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8007 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8008 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8009 mso-no-proof:yes'><o:p></o:p></span></p>
8011 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8012 style='mso-no-proof:yes'>-pdb_min_cov<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8013 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732351
8014 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8015 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8016 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350031000000</w:data>
8017 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8018 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8019 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8020 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8021 mso-no-proof:yes'><o:p></o:p></span></p>
8023 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8024 style='mso-no-proof:yes'>-pdb_db<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8025 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732352
8026 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8027 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8028 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350032000000</w:data>
8029 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8030 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8031 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8032 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8033 mso-no-proof:yes'><o:p></o:p></span></p>
8035 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8036 style='mso-no-proof:yes'>-pdb_type<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8037 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732353
8038 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8039 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8040 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350033000000</w:data>
8041 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8042 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8043 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8044 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8045 mso-no-proof:yes'><o:p></o:p></span></p>
8047 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8048 style='mso-no-proof:yes'>CPU Control<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
8049 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732354
8050 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8051 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8052 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350034000000</w:data>
8053 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8054 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8055 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8056 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8057 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8059 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8060 style='mso-no-proof:yes'>Multithreading<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8061 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732355
8062 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8063 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8064 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350035000000</w:data>
8065 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8066 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8067 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8068 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8069 mso-no-proof:yes'><o:p></o:p></span></p>
8071 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8072 style='mso-no-proof:yes'>-multi_core<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8073 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732356
8074 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8075 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8076 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350036000000</w:data>
8077 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8078 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8079 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8080 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8081 mso-no-proof:yes'><o:p></o:p></span></p>
8083 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8084 style='mso-no-proof:yes'>-n_core<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8085 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732357
8086 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8087 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8088 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350037000000</w:data>
8089 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8090 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8091 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8092 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8093 mso-no-proof:yes'><o:p></o:p></span></p>
8095 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8096 style='mso-no-proof:yes'>Limits<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8097 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732358
8098 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8099 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8100 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350038000000</w:data>
8101 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8102 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8103 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8104 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8105 mso-no-proof:yes'><o:p></o:p></span></p>
8107 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8108 style='mso-no-proof:yes'>-mem_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8109 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732359
8110 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8111 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8112 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350039000000</w:data>
8113 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8114 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8115 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8116 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8117 mso-no-proof:yes'><o:p></o:p></span></p>
8119 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8120 style='mso-no-proof:yes'>-ulimit<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8121 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732360
8122 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8123 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8124 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360030000000</w:data>
8125 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8126 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8127 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8128 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8129 mso-no-proof:yes'><o:p></o:p></span></p>
8131 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8132 style='mso-no-proof:yes'>-maxlen<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8133 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732361
8134 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8135 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8136 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360031000000</w:data>
8137 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8138 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8139 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8140 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8141 mso-no-proof:yes'><o:p></o:p></span></p>
8143 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8144 style='mso-no-proof:yes'>Aligning more than 100 sequences with DPA<span
8145 style='mso-tab-count:1 dotted'>......................................................................................................................... </span></span><!--[if supportFields]><span
8146 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732362
8147 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8148 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8149 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360032000000</w:data>
8150 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8151 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8152 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8153 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8154 mso-no-proof:yes'><o:p></o:p></span></p>
8156 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8157 style='mso-no-proof:yes'>-maxnseq<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8158 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732363
8159 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8160 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8161 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360033000000</w:data>
8162 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8163 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8164 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8165 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8166 mso-no-proof:yes'><o:p></o:p></span></p>
8168 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8169 style='mso-no-proof:yes'>-dpa_master_aln<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8170 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732364
8171 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8172 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8173 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360034000000</w:data>
8174 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8175 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8176 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8177 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8178 mso-no-proof:yes'><o:p></o:p></span></p>
8180 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8181 style='mso-no-proof:yes'>-dpa_maxnseq<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8182 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732365
8183 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8184 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8185 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360035000000</w:data>
8186 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8187 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8188 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8189 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8190 mso-no-proof:yes'><o:p></o:p></span></p>
8192 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8193 style='mso-no-proof:yes'>-dpa_min_score1<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8194 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732366
8195 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8196 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8197 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360036000000</w:data>
8198 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8199 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8200 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8201 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8202 mso-no-proof:yes'><o:p></o:p></span></p>
8204 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8205 style='mso-no-proof:yes'>-dpa_min_score2<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8206 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732367
8207 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8208 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8209 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360037000000</w:data>
8210 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8211 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8212 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8213 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8214 mso-no-proof:yes'><o:p></o:p></span></p>
8216 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8217 style='mso-no-proof:yes'>-dap_tree [NOT IMPLEMENTED]<span style='mso-tab-count:
8218 1 dotted'>.................................................................................................................................................... </span></span><!--[if supportFields]><span
8219 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732368
8220 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8221 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8222 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360038000000</w:data>
8223 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8224 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8225 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8226 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8227 mso-no-proof:yes'><o:p></o:p></span></p>
8229 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8230 style='mso-no-proof:yes'>Using Structures<span style='mso-tab-count:1 dotted'>.......................................................................................................................... </span></span><!--[if supportFields]><span
8231 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732369
8232 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8233 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8234 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360039000000</w:data>
8235 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8236 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8237 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8238 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8239 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8241 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8242 style='mso-no-proof:yes'>Generic<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8243 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732370
8244 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8245 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8246 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370030000000</w:data>
8247 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8248 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8249 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8250 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8251 mso-no-proof:yes'><o:p></o:p></span></p>
8253 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8254 style='mso-no-proof:yes'>-mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8255 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732371
8256 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8257 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8258 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370031000000</w:data>
8259 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8260 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8261 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8262 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8263 mso-no-proof:yes'><o:p></o:p></span></p>
8265 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8266 style='mso-no-proof:yes'>-check_pdb_status<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8267 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732372
8268 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8269 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8270 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370032000000</w:data>
8271 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8272 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8273 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8274 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8275 mso-no-proof:yes'><o:p></o:p></span></p>
8277 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8278 style='mso-no-proof:yes'>3D Coffee: Using SAP<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8279 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732373
8280 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8281 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8282 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370033000000</w:data>
8283 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8284 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8285 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8286 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8287 mso-no-proof:yes'><o:p></o:p></span></p>
8289 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8290 style='mso-no-proof:yes'>Using/finding PDB templates for the Sequences<span
8291 style='mso-tab-count:1 dotted'>................................................................................................................... </span></span><!--[if supportFields]><span
8292 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732374
8293 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8294 style='mso-no-proof:yes'>57<!--[if gte mso 9]><xml>
8295 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370034000000</w:data>
8296 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8297 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8298 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8299 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8300 mso-no-proof:yes'><o:p></o:p></span></p>
8302 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8303 style='mso-no-proof:yes'>-template_file<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8304 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732375
8305 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8306 style='mso-no-proof:yes'>57<!--[if gte mso 9]><xml>
8307 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370035000000</w:data>
8308 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8309 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8310 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8311 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8312 mso-no-proof:yes'><o:p></o:p></span></p>
8314 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8315 style='mso-no-proof:yes'>-struc_to_use<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8316 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732376
8317 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8318 style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
8319 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370036000000</w:data>
8320 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8321 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8322 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8323 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8324 mso-no-proof:yes'><o:p></o:p></span></p>
8326 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8327 style='mso-no-proof:yes'>Multiple Local Alignments<span style='mso-tab-count:
8328 1 dotted'>........................................................................................................... </span></span><!--[if supportFields]><span
8329 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732377
8330 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8331 style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
8332 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370037000000</w:data>
8333 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8334 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8335 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8336 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8337 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8339 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8340 style='mso-no-proof:yes'>-domain/-mocca<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8341 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732378
8342 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8343 style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
8344 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370038000000</w:data>
8345 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8346 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8347 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8348 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8349 mso-no-proof:yes'><o:p></o:p></span></p>
8351 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8352 style='mso-no-proof:yes'>-start<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8353 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732379
8354 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8355 style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
8356 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370039000000</w:data>
8357 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8358 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8359 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8360 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8361 mso-no-proof:yes'><o:p></o:p></span></p>
8363 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8364 style='mso-no-proof:yes'>-len<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8365 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732380
8366 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8367 style='mso-no-proof:yes'>60<!--[if gte mso 9]><xml>
8368 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380030000000</w:data>
8369 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8370 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8371 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8372 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8373 mso-no-proof:yes'><o:p></o:p></span></p>
8375 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8376 style='mso-no-proof:yes'>-scale<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8377 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732381
8378 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8379 style='mso-no-proof:yes'>60<!--[if gte mso 9]><xml>
8380 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380031000000</w:data>
8381 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8382 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8383 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8384 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8385 mso-no-proof:yes'><o:p></o:p></span></p>
8387 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8388 style='mso-no-proof:yes'>-domain_interactive [Examples]<span style='mso-tab-count:
8389 1 dotted'>...................................................................................................................................................... </span></span><!--[if supportFields]><span
8390 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732382
8391 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8392 style='mso-no-proof:yes'>60<!--[if gte mso 9]><xml>
8393 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380032000000</w:data>
8394 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8395 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8396 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8397 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8398 mso-no-proof:yes'><o:p></o:p></span></p>
8400 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8401 style='mso-no-proof:yes'>Output Control<span style='mso-tab-count:1 dotted'>............................................................................................................................. </span></span><!--[if supportFields]><span
8402 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732383
8403 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8404 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8405 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380033000000</w:data>
8406 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8407 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8408 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8409 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8410 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8412 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8413 style='mso-no-proof:yes'>Generic<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8414 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732384
8415 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8416 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8417 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380034000000</w:data>
8418 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8419 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8420 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8421 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8422 mso-no-proof:yes'><o:p></o:p></span></p>
8424 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8425 style='mso-no-proof:yes'>Conventions Regarding Filenames<span style='mso-tab-count:
8426 1 dotted'>................................................................................................................................................. </span></span><!--[if supportFields]><span
8427 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732385
8428 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8429 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8430 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380035000000</w:data>
8431 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8432 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8433 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8434 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8435 mso-no-proof:yes'><o:p></o:p></span></p>
8437 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8438 style='mso-no-proof:yes'>Identifying the Output files automatically<span
8439 style='mso-tab-count:1 dotted'>.................................................................................................................................. </span></span><!--[if supportFields]><span
8440 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732386
8441 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8442 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8443 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380036000000</w:data>
8444 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8445 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8446 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8447 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8448 mso-no-proof:yes'><o:p></o:p></span></p>
8450 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8451 style='mso-no-proof:yes'>-no_warning<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8452 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732387
8453 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8454 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8455 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380037000000</w:data>
8456 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8457 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8458 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8459 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8460 mso-no-proof:yes'><o:p></o:p></span></p>
8462 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8463 style='mso-no-proof:yes'>Alignments<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8464 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732388
8465 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8466 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8467 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380038000000</w:data>
8468 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8469 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8470 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8471 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8472 mso-no-proof:yes'><o:p></o:p></span></p>
8474 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8475 style='mso-no-proof:yes'>-outfile<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8476 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732389
8477 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8478 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8479 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380039000000</w:data>
8480 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8481 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8482 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8483 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8484 mso-no-proof:yes'><o:p></o:p></span></p>
8486 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8487 style='mso-no-proof:yes'>-output<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8488 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732390
8489 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8490 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8491 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390030000000</w:data>
8492 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8493 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8494 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8495 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8496 mso-no-proof:yes'><o:p></o:p></span></p>
8498 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8499 style='mso-no-proof:yes'>-outseqweight<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8500 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732391
8501 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8502 style='mso-no-proof:yes'>62<!--[if gte mso 9]><xml>
8503 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390031000000</w:data>
8504 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8505 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8506 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8507 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8508 mso-no-proof:yes'><o:p></o:p></span></p>
8510 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8511 style='mso-no-proof:yes'>-case<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8512 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732392
8513 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8514 style='mso-no-proof:yes'>62<!--[if gte mso 9]><xml>
8515 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390032000000</w:data>
8516 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8517 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8518 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8519 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8520 mso-no-proof:yes'><o:p></o:p></span></p>
8522 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8523 style='mso-no-proof:yes'>-cpu<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8524 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732393
8525 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8526 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8527 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390033000000</w:data>
8528 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8529 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8530 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8531 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8532 mso-no-proof:yes'><o:p></o:p></span></p>
8534 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8535 style='mso-no-proof:yes'>-outseqweight<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8536 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732394
8537 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8538 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8539 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390034000000</w:data>
8540 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8541 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8542 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8543 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8544 mso-no-proof:yes'><o:p></o:p></span></p>
8546 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8547 style='mso-no-proof:yes'>-outorder [cw]<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8548 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732395
8549 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8550 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8551 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390035000000</w:data>
8552 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8553 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8554 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8555 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8556 mso-no-proof:yes'><o:p></o:p></span></p>
8558 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8559 style='mso-no-proof:yes'>-inorder [cw]<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8560 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732396
8561 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8562 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8563 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390036000000</w:data>
8564 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8565 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8566 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8567 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8568 mso-no-proof:yes'><o:p></o:p></span></p>
8570 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8571 style='mso-no-proof:yes'>-seqnos<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8572 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732397
8573 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8574 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8575 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390037000000</w:data>
8576 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8577 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8578 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8579 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8580 mso-no-proof:yes'><o:p></o:p></span></p>
8582 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8583 style='mso-no-proof:yes'>Libraries<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8584 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732398
8585 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8586 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8587 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390038000000</w:data>
8588 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8589 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8590 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8591 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8592 mso-no-proof:yes'><o:p></o:p></span></p>
8594 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8595 style='mso-no-proof:yes'>-out_lib<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8596 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732399
8597 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8598 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8599 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390039000000</w:data>
8600 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8601 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8602 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8603 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8604 mso-no-proof:yes'><o:p></o:p></span></p>
8606 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8607 style='mso-no-proof:yes'>-lib_only<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8608 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732400
8609 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8610 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8611 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300030000000</w:data>
8612 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8613 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8614 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8615 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8616 mso-no-proof:yes'><o:p></o:p></span></p>
8618 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8619 style='mso-no-proof:yes'>Trees<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8620 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732401
8621 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8622 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8623 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300031000000</w:data>
8624 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8625 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8626 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8627 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8628 mso-no-proof:yes'><o:p></o:p></span></p>
8630 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8631 style='mso-no-proof:yes'>-newtree<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8632 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732402
8633 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8634 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8635 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300032000000</w:data>
8636 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8637 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8638 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8639 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8640 mso-no-proof:yes'><o:p></o:p></span></p>
8642 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8643 style='mso-no-proof:yes'>Reliability Estimation<span style='mso-tab-count:1 dotted'>................................................................................................................... </span></span><!--[if supportFields]><span
8644 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732403
8645 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8646 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8647 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300033000000</w:data>
8648 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8649 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8650 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8651 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8652 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8654 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8655 style='mso-no-proof:yes'>CORE Computation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8656 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732404
8657 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8658 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8659 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300034000000</w:data>
8660 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8661 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8662 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8663 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8664 mso-no-proof:yes'><o:p></o:p></span></p>
8666 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8667 style='mso-no-proof:yes'>-evaluate_mode<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8668 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732405
8669 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8670 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8671 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300035000000</w:data>
8672 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8673 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8674 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8675 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8676 mso-no-proof:yes'><o:p></o:p></span></p>
8678 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8679 style='mso-no-proof:yes'>Generic Output<span style='mso-tab-count:1 dotted'>............................................................................................................................ </span></span><!--[if supportFields]><span
8680 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732406
8681 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8682 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8683 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300036000000</w:data>
8684 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8685 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8686 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8687 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8688 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8690 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8691 style='mso-no-proof:yes'>-run_name<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8692 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732407
8693 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8694 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8695 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300037000000</w:data>
8696 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8697 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8698 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8699 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8700 mso-no-proof:yes'><o:p></o:p></span></p>
8702 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8703 style='mso-no-proof:yes'>-quiet<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8704 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732408
8705 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8706 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8707 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300038000000</w:data>
8708 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8709 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8710 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8711 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8712 mso-no-proof:yes'><o:p></o:p></span></p>
8714 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8715 style='mso-no-proof:yes'>-align [CW]<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8716 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732409
8717 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8718 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8719 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300039000000</w:data>
8720 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8721 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8722 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8723 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8724 mso-no-proof:yes'><o:p></o:p></span></p>
8726 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8727 style='mso-no-proof:yes'>APDB, iRMSD and tRMSD Parameters<span
8728 style='mso-tab-count:1 dotted'>........................................................................................ </span></span><!--[if supportFields]><span
8729 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732410
8730 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8731 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8732 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310030000000</w:data>
8733 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8734 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8735 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8736 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8737 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8739 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8740 style='mso-no-proof:yes'>-quiet [Same as T-Coffee]<span style='mso-tab-count:
8741 1 dotted'>..................................................................................................................................................................... </span></span><!--[if supportFields]><span
8742 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732411
8743 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8744 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8745 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310031000000</w:data>
8746 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8747 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8748 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8749 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8750 mso-no-proof:yes'><o:p></o:p></span></p>
8752 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8753 style='mso-no-proof:yes'>-run_name [Same as T-Coffee]<span style='mso-tab-count:
8754 1 dotted'>.......................................................................................................................................................... </span></span><!--[if supportFields]><span
8755 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732412
8756 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8757 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8758 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310032000000</w:data>
8759 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8760 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8761 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8762 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8763 mso-no-proof:yes'><o:p></o:p></span></p>
8765 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8766 style='mso-no-proof:yes'>-aln<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8767 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732413
8768 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8769 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8770 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310033000000</w:data>
8771 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8772 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8773 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8774 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8775 mso-no-proof:yes'><o:p></o:p></span></p>
8777 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8778 style='mso-no-proof:yes'>-n_excluded_nb<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8779 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732414
8780 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8781 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8782 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310034000000</w:data>
8783 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8784 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8785 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8786 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8787 mso-no-proof:yes'><o:p></o:p></span></p>
8789 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8790 style='mso-no-proof:yes'>-maximum_distance<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8791 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732415
8792 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8793 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8794 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310035000000</w:data>
8795 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8796 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8797 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8798 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8799 mso-no-proof:yes'><o:p></o:p></span></p>
8801 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8802 style='mso-no-proof:yes'>-similarity_threshold<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................. </span></span><!--[if supportFields]><span
8803 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732416
8804 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8805 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8806 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310036000000</w:data>
8807 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8808 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8809 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8810 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8811 mso-no-proof:yes'><o:p></o:p></span></p>
8813 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8814 style='mso-no-proof:yes'>-local_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8815 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732417
8816 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8817 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8818 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310037000000</w:data>
8819 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8820 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8821 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8822 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8823 mso-no-proof:yes'><o:p></o:p></span></p>
8825 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8826 style='mso-no-proof:yes'>-filter<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8827 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732418
8828 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8829 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8830 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310038000000</w:data>
8831 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8832 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8833 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8834 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8835 mso-no-proof:yes'><o:p></o:p></span></p>
8837 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8838 style='mso-no-proof:yes'>-print_rapdb [Unsupported]<span style='mso-tab-count:
8839 1 dotted'>.............................................................................................................................................................. </span></span><!--[if supportFields]><span
8840 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732419
8841 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8842 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8843 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310039000000</w:data>
8844 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8845 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8846 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8847 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8848 mso-no-proof:yes'><o:p></o:p></span></p>
8850 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8851 style='mso-no-proof:yes'>-outfile [Same as T-Coffee]<span style='mso-tab-count:
8852 1 dotted'>.................................................................................................................................................................. </span></span><!--[if supportFields]><span
8853 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732420
8854 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8855 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8856 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320030000000</w:data>
8857 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8858 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8859 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8860 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8861 mso-no-proof:yes'><o:p></o:p></span></p>
8863 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8864 style='mso-no-proof:yes'>-color_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8865 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732421
8866 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8867 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8868 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320031000000</w:data>
8869 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8870 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8871 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8872 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8873 mso-no-proof:yes'><o:p></o:p></span></p>
8875 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8876 style='mso-no-proof:yes'>Environment Variables<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
8877 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732422
8878 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8879 style='mso-no-proof:yes'>68<!--[if gte mso 9]><xml>
8880 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320032000000</w:data>
8881 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8882 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8883 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8884 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8885 mso-no-proof:yes'><o:p></o:p></span></p>
8887 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8888 style='mso-no-proof:yes'>Output of the .dnd file.<span style='mso-tab-count:
8889 1 dotted'>............................................................................................................................................................................ </span></span><!--[if supportFields]><span
8890 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732423
8891 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8892 style='mso-no-proof:yes'>69<!--[if gte mso 9]><xml>
8893 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320033000000</w:data>
8894 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8895 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8896 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8897 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8898 mso-no-proof:yes'><o:p></o:p></span></p>
8900 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8901 style='mso-no-proof:yes'>Permissions<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8902 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732424
8903 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8904 style='mso-no-proof:yes'>69<!--[if gte mso 9]><xml>
8905 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320034000000</w:data>
8906 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8907 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8908 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8909 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8910 mso-no-proof:yes'><o:p></o:p></span></p>
8912 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8913 style='mso-no-proof:yes'>Other Programs<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8914 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732425
8915 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8916 style='mso-no-proof:yes'>69<!--[if gte mso 9]><xml>
8917 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320035000000</w:data>
8918 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8919 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8920 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8921 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8922 mso-no-proof:yes'><o:p></o:p></span></p>
8924 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8925 style='mso-no-proof:yes'>Parameter files<span style='mso-tab-count:1 dotted'>............................................................................................................................ </span></span><!--[if supportFields]><span
8926 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732426
8927 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8928 style='mso-no-proof:yes'>70<!--[if gte mso 9]><xml>
8929 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320036000000</w:data>
8930 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8931 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8932 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8933 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8934 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8936 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8937 style='mso-no-proof:yes'>Sequence Name Handling<span style='mso-tab-count:1 dotted'>........................................................................................................... </span></span><!--[if supportFields]><span
8938 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732427
8939 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8940 style='mso-no-proof:yes'>70<!--[if gte mso 9]><xml>
8941 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320037000000</w:data>
8942 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8943 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8944 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8945 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8946 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8948 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8949 style='mso-no-proof:yes'>Automatic Format Recognition<span style='mso-tab-count:
8950 1 dotted'>................................................................................................... </span></span><!--[if supportFields]><span
8951 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732428
8952 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8953 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
8954 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320038000000</w:data>
8955 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8956 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8957 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8958 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8959 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8961 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8962 style='mso-no-proof:yes'>Structures<span style='mso-tab-count:1 dotted'>.................................................................................................................................... </span></span><!--[if supportFields]><span
8963 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732429
8964 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8965 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
8966 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320039000000</w:data>
8967 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8968 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8969 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8970 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8971 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8973 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8974 style='mso-no-proof:yes'>RNA Structures<span style='mso-tab-count:1 dotted'>............................................................................................................................. </span></span><!--[if supportFields]><span
8975 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732430
8976 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8977 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
8978 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330030000000</w:data>
8979 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8980 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8981 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8982 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8983 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8985 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8986 style='mso-no-proof:yes'>Sequences<span style='mso-tab-count:1 dotted'>.................................................................................................................................... </span></span><!--[if supportFields]><span
8987 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732431
8988 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8989 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
8990 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330031000000</w:data>
8991 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8992 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8993 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8994 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8995 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8997 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8998 style='mso-no-proof:yes'>Alignments<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
8999 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732432
9000 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9001 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
9002 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330032000000</w:data>
9003 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9004 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9005 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9006 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9007 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9009 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9010 style='mso-no-proof:yes'>Libraries<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
9011 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732433
9012 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9013 style='mso-no-proof:yes'>72<!--[if gte mso 9]><xml>
9014 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330033000000</w:data>
9015 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9016 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9017 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9018 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9019 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9021 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9022 style='mso-no-proof:yes'>T-COFFEE_LIB_FORMAT_01<span style='mso-tab-count:1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
9023 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732434
9024 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9025 style='mso-no-proof:yes'>72<!--[if gte mso 9]><xml>
9026 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330034000000</w:data>
9027 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9028 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9029 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9030 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9031 mso-no-proof:yes'><o:p></o:p></span></p>
9033 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9034 style='mso-no-proof:yes'>T-COFFEE_LIB_FORMAT_02<span style='mso-tab-count:1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
9035 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732435
9036 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9037 style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
9038 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330035000000</w:data>
9039 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9040 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9041 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9042 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9043 mso-no-proof:yes'><o:p></o:p></span></p>
9045 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9046 style='mso-no-proof:yes'>Library List<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
9047 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732436
9048 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9049 style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
9050 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330036000000</w:data>
9051 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9052 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9053 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9054 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9055 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9057 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9058 style='mso-no-proof:yes'>Substitution matrices.<span style='mso-tab-count:1 dotted'>................................................................................................................. </span></span><!--[if supportFields]><span
9059 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732437
9060 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9061 style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
9062 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330037000000</w:data>
9063 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9064 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9065 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9066 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9067 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9069 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9070 style='mso-no-proof:yes'>ClustalW Style [Deprecated]<span style='mso-tab-count:
9071 1 dotted'>.............................................................................................................................................................. </span></span><!--[if supportFields]><span
9072 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732438
9073 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9074 style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
9075 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330038000000</w:data>
9076 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9077 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9078 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9079 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9080 mso-no-proof:yes'><o:p></o:p></span></p>
9082 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9083 style='mso-no-proof:yes'>BLAST Format [Recommended]<span style='mso-tab-count:
9084 1 dotted'>..................................................................................................................................................... </span></span><!--[if supportFields]><span
9085 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732439
9086 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9087 style='mso-no-proof:yes'>74<!--[if gte mso 9]><xml>
9088 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330039000000</w:data>
9089 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9090 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9091 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9092 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9093 mso-no-proof:yes'><o:p></o:p></span></p>
9095 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9096 style='mso-no-proof:yes'>Sequences Weights<span style='mso-tab-count:1 dotted'>..................................................................................................................... </span></span><!--[if supportFields]><span
9097 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732440
9098 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9099 style='mso-no-proof:yes'>74<!--[if gte mso 9]><xml>
9100 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340030000000</w:data>
9101 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9102 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9103 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9104 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9105 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9107 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9108 style='mso-no-proof:yes'>Development<span style='mso-tab-count:1 dotted'>............................................................................................................................... </span></span><!--[if supportFields]><span
9109 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732441
9110 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9111 style='mso-no-proof:yes'>76<!--[if gte mso 9]><xml>
9112 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340031000000</w:data>
9113 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9114 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9115 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9116 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9117 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9119 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
9120 style='mso-no-proof:yes'>profile2list<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
9121 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732442
9122 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9123 style='mso-no-proof:yes'>76<!--[if gte mso 9]><xml>
9124 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340032000000</w:data>
9125 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9126 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9127 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9128 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9129 mso-no-proof:yes'><o:p></o:p></span></p>
9131 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9132 style='mso-no-proof:yes'>Command Line List<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
9133 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732443
9134 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9135 style='mso-no-proof:yes'>76<!--[if gte mso 9]><xml>
9136 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340033000000</w:data>
9137 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9138 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9139 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9140 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9141 mso-no-proof:yes'><o:p></o:p></span></p>
9143 <p class=FAQ><!--[if supportFields]><span lang=EN-GB><span style='mso-element:
9144 field-end'></span></span><![endif]--></p>
9148 <b style='mso-bidi-font-weight:normal'><span lang=EN-GB style='font-size:11.0pt;
9149 mso-bidi-font-size:14.0pt;font-family:"Comic Sans MS";mso-fareast-font-family:
9150 "Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:EN-GB;
9151 mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:auto;
9152 mso-break-type:section-break'>
9155 <div class=Section4>
9157 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
9158 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
9161 <p class=ChapterTitle><a name="_Toc101065185"></a><a name="_Toc102494650"><span
9162 style='mso-bookmark:_Toc101065185'>License and Terms of Use</span></a></p>
9166 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9168 <h2><a name="_Toc102494275"></a><a name="_Toc102494651"></a><a
9169 name="_Toc151732187"><span style='mso-bookmark:_Toc102494651'><span
9170 style='mso-bookmark:_Toc102494275'>T-Coffee is distributed under the Gnu Public
9171 License</span></span></a></h2>
9173 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9175 <p class=MyNormal><span lang=AF>Please make sure you have agreed with the terms
9176 of the license attached to the package before using the T-Coffee package or its
9177 documentation. T-Coffee is a freeware open source distributed under a GPL
9178 license. This means that there are very little restrictions to its use, either
9179 in an academic or a non academic environment.</span></p>
9181 <h2><a name="_Toc102494276"></a><a name="_Toc102494652"></a><a
9182 name="_Toc151732188"><span style='mso-bookmark:_Toc102494652'><span
9183 style='mso-bookmark:_Toc102494276'>T-Coffee code can be re-used freely</span></span></a></h2>
9185 <p class=MyNormal><span lang=AF>Our philosophy is that code is meant to be
9186 re-used, including ours. No permission is needed for the cut and paste of a few
9187 functions, although we are always happy to receive pieces of improved code.</span></p>
9189 <h2><a name="_Toc101065186"></a><a name="_Toc102494653"></a><a
9190 name="_Toc151732189"><span style='mso-bookmark:_Toc102494653'><span
9191 style='mso-bookmark:_Toc101065186'>T-Coffee can be incorporated in most
9192 pipelines: Plug-in/Plug-out
\85</span></span></a><span style='mso-bookmark:_Toc102494653'><span
9193 style='mso-bookmark:_Toc101065186'></span></span></h2>
9195 <p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
9196 style='mso-bookmark:_Toc101065186'><span lang=AF>Our philosophy is to insure
9197 that as many methods as possible can be used as plug-ins within T-Coffee.
9198 Likewise, we will give as much support as possible to anyone wishing to turn
9199 T-Coffee into a plug-in for another method. For more details on how to do this,
9200 see the plug-in and the plug-out sections of the Tutorial Manual.</span></span></span></p>
9202 <p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
9203 style='mso-bookmark:_Toc101065186'><span lang=AF>Again, you do not need our
9204 permission to either use T-Coffee (or your method as a plug-in/out) but if you
9205 let us know, we will insure the stability of T-Coffee within your system
9206 through future releases. </span></span></span></p>
9208 <p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
9209 style='mso-bookmark:_Toc101065186'><span lang=AF>The current license only
9210 allows for the incorporation of T-Coffee in non-commercial pipelines (i.e.
9211 where you do not sell the pipeline, or access to it). If your pipeline is
9212 commercial, please get in touch with us. </span></span></span></p>
9214 <p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
9215 style='mso-bookmark:_Toc101065186'><span lang=AF><o:p> </o:p></span></span></span></p>
9217 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
9218 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
9221 <p class=ChapterTitle><span style='mso-bookmark:_Toc102494653'><span
9222 style='mso-bookmark:_Toc101065186'>Addresses and Contacts</span></span><span
9223 style='mso-bookmark:_Toc101065186'></span><span style='mso-bookmark:_Toc102494653'></span><span
9224 style='font-size:98.0pt;mso-bidi-font-size:48.0pt'><o:p></o:p></span></p>
9228 <h2><a name="_Toc151732190">Contributors</a></h2>
9230 <p class=MsoBodyText>T-coffee is developed, maintained, monitored, used and
9231 debugged by a dedicated team that include or have included:</p>
9233 <p class=MsoBodyText><span style='mso-tab-count:1'> </span>Cédric
9234 Notredame, Paolo di Tomasso, Jean-François Taly, Cedrik Magis, Fabrice
9235 Armougom, Des Higgins, Sebastien Moretti, Orla O
\92Sullivan. Eamon O
\92Toole,
9236 Olivier Poirot, Karsten Suhre, Iain Wallace, Andreas Wilm</p>
9238 <h2><a name="_Toc151732191">Addresses</a></h2>
9240 <p class=MyNormal><span lang=AF>We are always very eager to get some user
9241 feedback. Please do not hesitate to drop us a line<span style="mso-spacerun:
9242 yes"> </span>at: <a href="mailto:cedric.notredame@europe.com"><span
9243 lang=EN-US style='mso-ansi-language:EN-US'>cedric.notredame@europe.com</span></a>
9244 The latest updates of T-Coffee are always available<span style="mso-spacerun:
9245 yes"> </span>on: www.tcoffee.org . On this address you will also find a
9246 link to some of the online T-Coffee servers, including Tcoffee@igs </span></p>
9248 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9250 <p class=MyNormal><span lang=AF>T-Coffee can be used to automatically check if
9251 an updated version is available, however the program will not update
9252 automatically, as this can cause endless reproducibility problems.</span></p>
9254 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9255 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9256 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9257 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9259 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
9264 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9266 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
9267 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
9270 <p class=ChapterTitle><a name="_Toc101065187"></a><a name="_Toc102494654"><span
9271 style='mso-bookmark:_Toc101065187'>Citations</span></a></p>
9275 <p class=MyNormal><span lang=AF>It is important that you cite T-Coffee when you
9276 use it. Citing us is (almost) like giving us money: it helps us convincing our
9277 institutions that what we do is useful and that they should keep paying our
9278 salaries and deliver Donuts to our offices from time to time (Not that they
9279 ever did it, but it would be nice anyway). </span></p>
9281 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9283 <p class=MyNormal><span lang=AF>Cite the server if you used it, otherwise, cite
9284 the original paper from 2000 (No, it was never named "T-Coffee
9285 2000").</span></p>
9287 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9288 style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9289 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9290 <td width="53%" style='width:53.48%;padding:0cm 0cm 0cm 0cm'>
9291 <p class=MyNormalJustified><a
9292 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570">Notredame
9293 C, Higgins DG, Heringa J.</a><span style='mso-bidi-font-size:12.0pt;
9294 color:black'><o:p></o:p></span></p>
9296 <td width="43%" nowrap valign=top style='width:43.3%;padding:0cm 0cm 0cm 0cm'>
9297 <p class=MyNormalJustified><a
9298 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=10964570"><span
9299 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shapetype
9300 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
9301 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
9302 <v:stroke joinstyle="miter"/>
9304 <v:f eqn="if lineDrawn pixelLineWidth 0"/>
9305 <v:f eqn="sum @0 1 0"/>
9306 <v:f eqn="sum 0 0 @1"/>
9307 <v:f eqn="prod @2 1 2"/>
9308 <v:f eqn="prod @3 21600 pixelWidth"/>
9309 <v:f eqn="prod @3 21600 pixelHeight"/>
9310 <v:f eqn="sum @0 0 1"/>
9311 <v:f eqn="prod @6 1 2"/>
9312 <v:f eqn="prod @7 21600 pixelWidth"/>
9313 <v:f eqn="sum @8 21600 0"/>
9314 <v:f eqn="prod @7 21600 pixelHeight"/>
9315 <v:f eqn="sum @10 21600 0"/>
9317 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
9318 <o:lock v:ext="edit" aspectratio="t"/>
9319 </v:shapetype><v:shape id="_x0000_i1025" type="#_x0000_t75" style='width:15pt;
9320 height:11pt;visibility:hidden' print="f">
9321 <v:imagedata src="t_coffee_technical_files/image001.png" o:title="邐潎浲污退慆x0邐1"/>
9322 <o:lock v:ext="edit" grouping="t"/>
9323 </v:shape><![endif]--><!--[if gte vml 1]><v:shape id="_x0000_i1026" type="#_x0000_t75"
9324 style='width:15pt;height:11pt;visibility:hidden' print="f">
9325 <v:imagedata src="t_coffee_technical_files/image002.png" o:title="邐潎浲污退慆x0邐1"/>
9326 <o:lock v:ext="edit" grouping="t"/>
9327 </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu10964570\)\;\0022 \\t \0022_self\0022"'><span
9328 class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9329 <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9332 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9333 <td width="97%" colspan=2 style='width:97.86%;padding:0cm 0cm 0cm 0cm'>
9334 <p class=MyNormalJustified>T-Coffee: A novel method for fast and accurate
9335 multiple sequence alignment.<br>
9336 J Mol Biol. 2000 Sep 8;302(1):205-17. <br>
9337 PMID: 10964570 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9338 12.0pt;color:black'><o:p></o:p></span></p>
9343 <p class=MyNormal><span lang=AF>Other useful publications include:</span></p>
9345 <h2><a name="_Toc101065188"></a><a name="_Toc102494277"></a><a
9346 name="_Toc102494655"></a><a name="_Toc151732192"><span style='mso-bookmark:
9347 _Toc102494655'><span style='mso-bookmark:_Toc102494277'><span style='mso-bookmark:
9348 _Toc101065188'>T-Coffee</span></span></span></a></h2>
9350 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9351 style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9352 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9353 <td width="53%" style='width:53.48%;padding:0cm 0cm 0cm 0cm'>
9354 <p class=MyNormalJustified><a
9355 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215460">Claude
9356 JB, Suhre K, Notredame C, Claverie JM, Abergel C.</a><span style='mso-bidi-font-size:
9357 12.0pt;color:black'><o:p></o:p></span></p>
9359 <td width="43%" nowrap valign=top style='width:43.3%;padding:0cm 0cm 0cm 0cm'>
9360 <p class=MyNormalJustified><a
9361 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15215460"><span
9362 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9363 id="_x0000_i1027" type="#_x0000_t75" style='width:15pt;height:11pt;
9364 visibility:hidden' print="f">
9365 <v:imagedata src="t_coffee_technical_files/image003.png" o:title="邐潎浲污退慆x0邐1"/>
9366 <o:lock v:ext="edit" grouping="t"/>
9367 </v:shape><![endif]--><!--[if gte vml 1]><v:shape id="_x0000_i1028" type="#_x0000_t75"
9368 style='width:15pt;height:11pt;visibility:hidden' print="f">
9369 <v:imagedata src="t_coffee_technical_files/image004.png" o:title="邐潎浲污退慆x0邐1"/>
9370 <o:lock v:ext="edit" grouping="t"/>
9371 </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu15215460\)\;\0022 \\t \0022_self\0022"'><span
9372 class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9373 <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9376 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9377 <td width="97%" colspan=2 style='width:97.86%;padding:0cm 0cm 0cm 0cm'>
9378 <p class=MyNormalJustified>CaspR: a web server for automated molecular
9379 replacement using homology modelling.<br>
9380 Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9. <br>
9381 PMID: 15215460 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9382 12.0pt;color:black'><o:p></o:p></span></p>
9387 <p class=MyNormalJustified><o:p> </o:p></p>
9389 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9390 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9391 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9392 <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9393 <p class=MyNormalJustified><a
9394 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215345">Poirot
9395 O, Suhre K, Abergel C, O'Toole E, Notredame C.</a><span style='mso-bidi-font-size:
9396 12.0pt;color:black'><o:p></o:p></span></p>
9398 <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9399 <p class=MyNormalJustified><a
9400 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15215345"><span
9401 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9402 id="_x0000_i1029" type="#_x0000_t75" style='width:15pt;height:11pt;
9403 visibility:hidden' print="f">
9404 <v:imagedata src="t_coffee_technical_files/image005.png" o:title="邐潎浲污退慆x0邐1"/>
9405 <o:lock v:ext="edit" grouping="t"/>
9406 </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu15215345\)\;\0022 \\t \0022_self\0022"'><span
9407 class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9408 <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9411 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9412 <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9413 <p class=MyNormalJustified>3DCoffee@igs: a web server for combining sequences
9414 and structures into a multiple sequence alignment.<br>
9415 Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. <br>
9416 PMID: 15215345 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9417 12.0pt;color:black'><o:p></o:p></span></p>
9422 <p class=MyNormalJustified><o:p> </o:p></p>
9424 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9425 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9426 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9427 <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9428 <p class=MyNormalJustified><a
9429 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15201059">O'Sullivan
9430 O, Suhre K, Abergel C, Higgins DG, Notredame C.</a><span style='mso-bidi-font-size:
9431 12.0pt;color:black'><o:p></o:p></span></p>
9433 <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9434 <p class=MyNormalJustified><a
9435 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15201059"><span
9436 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9437 id="_x0000_i1030" type="#_x0000_t75" style='width:15pt;height:11pt;
9438 visibility:hidden' print="f">
9439 <v:imagedata src="t_coffee_technical_files/image006.png" o:title="邐潎浲污退慆x0邐1"/>
9440 <o:lock v:ext="edit" grouping="t"/>
9441 </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu15201059\)\;\0022 \\t \0022_self\0022"'><span
9442 class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9443 <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9446 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9447 <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9448 <p class=MyNormalJustified>3DCoffee: combining protein sequences and
9449 structures within multiple sequence alignments.<br>
9450 J Mol Biol. 2004 Jul 2;340(2):385-95. <br>
9451 PMID: 15201059 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9452 12.0pt;color:black'><o:p></o:p></span></p>
9457 <p class=MyNormalJustified><o:p> </o:p></p>
9459 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9460 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9461 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9462 <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9463 <p class=MyNormalJustified><a
9464 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12824354">Poirot
9465 O, O'Toole E, Notredame C.</a><span style='mso-bidi-font-size:12.0pt;
9466 color:black'><o:p></o:p></span></p>
9468 <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9469 <p class=MyNormalJustified><a
9470 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=12824354"><span
9471 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9472 id="_x0000_i1031" type="#_x0000_t75" style='width:15pt;height:11pt;
9473 visibility:hidden' print="f">
9474 <v:imagedata src="t_coffee_technical_files/image007.png" o:title="邐潎浲污退慆x0邐1"/>
9475 <o:lock v:ext="edit" grouping="t"/>
9476 </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu12824354\)\;\0022 \\t \0022_self\0022"'><span
9477 class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9478 <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9481 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9482 <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9483 <p class=MyNormalJustified>Tcoffee@igs: A web server for computing,
9484 evaluating and combining multiple sequence alignments.<br>
9485 Nucleic Acids Res. 2003 Jul 1;31(13):3503-6. <br>
9486 PMID: 12824354 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9487 12.0pt;color:black'><o:p></o:p></span></p>
9492 <p class=MyNormalJustified><o:p> </o:p></p>
9494 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9495 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9496 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9497 <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9498 <p class=MyNormalJustified><a
9499 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11301309">Notredame
9500 C.</a><span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9502 <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9503 <p class=MyNormalJustified><a
9504 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=11301309"><span
9505 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9506 id="_x0000_i1032" type="#_x0000_t75" style='width:15pt;height:11pt;
9507 visibility:hidden' print="f">
9508 <v:imagedata src="t_coffee_technical_files/image008.png" o:title="邐潎浲污退慆x0邐1"/>
9509 <o:lock v:ext="edit" grouping="t"/>
9510 </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu11301309\)\;\0022 \\t \0022_self\0022"'><span
9511 class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9512 <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9515 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9516 <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9517 <p class=MyNormalJustified>Mocca: semi-automatic method for domain hunting.<br>
9518 Bioinformatics. 2001 Apr;17(4):373-4. <br>
9519 PMID: 11301309 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9520 12.0pt;color:black'><o:p></o:p></span></p>
9525 <p class=MyNormalJustified><o:p> </o:p></p>
9527 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9528 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9529 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9530 <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9531 <p class=MyNormalJustified><a
9532 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570">Notredame
9533 C, Higgins DG, Heringa J.</a><span style='mso-bidi-font-size:12.0pt;
9534 color:black'><o:p></o:p></span></p>
9536 <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9537 <p class=MyNormalJustified><a
9538 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=10964570"><span
9539 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9540 id="_x0000_i1033" type="#_x0000_t75" style='width:15pt;height:11pt;
9541 visibility:hidden' print="f">
9542 <v:imagedata src="t_coffee_technical_files/image009.png" o:title="邐潎浲污退慆x0邐1"/>
9543 <o:lock v:ext="edit" grouping="t"/>
9544 </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu10964570\)\;\0022 \\t \0022_self\0022"'><span
9545 class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9546 <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9549 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9550 <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9551 <p class=MyNormalJustified>T-Coffee: A novel method for fast and accurate
9552 multiple sequence alignment.<br>
9553 J Mol Biol. 2000 Sep 8;302(1):205-17. <br>
9554 PMID: 10964570 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9555 12.0pt;color:black'><o:p></o:p></span></p>
9560 <p class=MyNormalJustified><o:p> </o:p></p>
9562 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9563 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9564 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9565 <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9566 <p class=MyNormalJustified><a
9567 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9682054">Notredame
9568 C, Holm L, Higgins DG.</a><span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9570 <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9571 <p class=MyNormalJustified><a
9572 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=9682054"><span
9573 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9574 id="_x0000_i1034" type="#_x0000_t75" style='width:15pt;height:11pt;
9575 visibility:hidden' print="f">
9576 <v:imagedata src="t_coffee_technical_files/image010.png" o:title="邐潎浲污退慆x0邐1"/>
9577 <o:lock v:ext="edit" grouping="t"/>
9578 </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu9682054\)\;\0022 \\t \0022_self\0022"'><span
9579 class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9580 <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9583 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9584 <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9585 <p class=MyNormalJustified>COFFEE: an objective function for multiple
9586 sequence alignments.<br>
9587 Bioinformatics. 1998 Jun;14(5):407-22. <br>
9588 PMID: 9682054 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9589 12.0pt;color:black'><o:p></o:p></span></p>
9594 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9596 <h2><a name="_Toc101065189"></a><a name="_Toc102494278"></a><a
9597 name="_Toc102494656"></a><a name="_Toc151732193"><span style='mso-bookmark:
9598 _Toc102494656'><span style='mso-bookmark:_Toc102494278'><span style='mso-bookmark:
9599 _Toc101065189'>Mocca</span></span></span></a></h2>
9601 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9602 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9603 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9604 <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9605 <p class=MyNormal><span lang=AF><a
9606 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11301309"><span
9607 lang=EN-US style='mso-ansi-language:EN-US'>Notredame C.</span></a></span><span
9608 lang=AF style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9610 <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9611 <p class=MyNormal><span lang=AF><a
9612 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=11301309&tool=ExternalSearch"><span
9613 lang=EN-US style='mso-bidi-font-size:9.0pt;color:#336699;mso-ansi-language:
9614 EN-US'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape id="_x0000_i1035"
9615 type="#_x0000_t75" style='width:15pt;height:11pt;visibility:hidden' print="f">
9616 <v:imagedata src="t_coffee_technical_files/image011.png" o:title="邐潎浲污退慆x0邐1"/>
9617 <o:lock v:ext="edit" grouping="t"/>
9618 </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu11301309\)\;\0022 \\t \0022_self\0022"'><span
9619 class=MsoHyperlink><span lang=EN-US style='mso-bidi-font-size:9.0pt;
9620 color:#336699;mso-ansi-language:EN-US'>Links</span></span></span> </span><span
9621 lang=AF style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9624 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9625 <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9626 <p class=MyNormal><span lang=AF>Mocca: semi-automatic method for domain
9628 Bioinformatics. 2001 Apr;17(4):373-4. <br>
9629 PMID: 11301309 [PubMed - indexed for MEDLINE]</span><span lang=AF
9630 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9635 <h2><a name="_Toc102494279"></a><a name="_Toc102494657"></a><a
9636 name="_Toc151732194"><span style='mso-bookmark:_Toc102494657'><span
9637 style='mso-bookmark:_Toc102494279'>CORE</span></span></a></h2>
9639 <p class=MyNormal><span lang=AF><a
9640 href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US
9641 style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf<o:p></o:p></span></a></span></p>
9643 <h2><a name="_Toc101065367"></a><a name="_Toc102494280"></a><a
9644 name="_Toc102494658"><span style='mso-bookmark:_Toc102494280'><span
9645 style='mso-bookmark:_Toc101065367'></span></span></a><a name="_Toc151732195"><span
9646 style='mso-bookmark:_Toc101065367'><span style='mso-bookmark:_Toc102494280'><span
9647 style='mso-bookmark:_Toc102494658'>Other Contributions</span></span></span></a></h2>
9649 <p class=MyNormal><span lang=AF>We do not mean to steal code, but we will
9650 always try to re-use pre-existing code whenever that code exists, free of
9651 copyright, just like we expect people to do with our code. However, whenever
9652 this happens, we make a point at properly citing the source of the original
9653 contribution. If ever you recognize a piece of your code improperly cited,
9654 please drop us a note and we will be happy to correct that.</span></p>
9656 <p class=MyNormal><span lang=AF>In the mean time, here are some important
9657 pieces of code from other packages that have been incorporated within the
9658 T-Coffee package. These include: </span></p>
9660 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-The
9661 Sim algorithm of Huang and Miller that given two sequences computes the N best
9662 scoring local alignments.</span></p>
9664 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-The
9665 tree reading/computing routines are taken from the ClustalW Package, courtesy
9666 of Julie Thompson, Des Higgins and Toby Gibson (Thompson, Higgins, Gibson,
9667 1994, 4673-4680,vol. 22, Nucleic Acid Research).</span></p>
9669 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-The
9670 implementation of the algorithm for aligning two sequences in linear space was
9671 adapted from Myers and Miller, in CABIOS, 1988, 11-17, vol. 1)</span></p>
9673 <p class=MyNormal><span lang=AF><span style="mso-spacerun: yes"> </span><span
9674 style='mso-tab-count:1'> </span>-Various
9675 techniques and algorithms have been implemented. Whenever relevant, the source
9676 of the code/algorithm/idea is indicated in the corresponding function.</span></p>
9678 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-64
9679 Bits compliance was implemented by Benjamin Sohn, Performance Computing Center
9680 Stuttgart (HLRS), Germany</span></p>
9682 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-David
9683 Mathog (Caltech) provided many fixes and useful feedback for improving the code
9684 and making the whole soft behaving more rationally</span></p>
9686 <h2><a name="_Toc151732196">Bug Reports and Feedback</a></h2>
9688 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-Prof
9689 David Jones (UCL) reported and corrected the PDB1K bug (now t_coffee/sap can
9690 align PDB sequences longer than 1000 AA).</span></p>
9692 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-Johan
9693 Leckner reported several bugs related to the treatment of PDB structures,
9694 insuring a consistent behavior between version 1.37 and current ones.</span></p>
9696 <p class=MyNormal><span lang=AF><span style="mso-spacerun: yes"> </span></span></p>
9698 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9700 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
9701 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
9704 <p class=ChapterTitle><a name="_Toc101065204"></a><a name="_Toc102494673"><span
9705 style='mso-bookmark:_Toc101065204'>I</span></a>nstallation of The T-Coffee
9710 <h2><a name="_Toc101065205"></a><a name="_Toc102494294"></a><a
9711 name="_Toc102494674"></a><a name="_Toc151732197"><span style='mso-bookmark:
9712 _Toc102494674'><span style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:
9713 _Toc101065205'>Third Party Packages and On Demand Installations</span></span></span></a><span
9714 style='mso-bookmark:_Toc102494674'><span style='mso-bookmark:_Toc102494294'><span
9715 style='mso-bookmark:_Toc101065205'></span></span></span></h2>
9717 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc102494674'><span
9718 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc101065205'><span
9719 lang=AF>T-Coffee is a complex package that interacts with many other third part
9720 software. If you only want a standalone version of T-Coffee, you may install
9721 that package on its own. If you want to use a most sophisticated flavor
9722 (3dcoffee, expresso, rcofeee, etc...), the installer will try to install all
9723 the third party packages required.</span></span></span></span></p>
9725 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc102494674'><span
9726 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc101065205'><span
9727 lang=AF>Note that since version 7.56, T-Coffee will use 'on demand'
9728 installation and install the third party packages it needs *when* it needs
9729 them. This only works for packages not requiring specific licenses and that can
9730 be installed by the regular installer. Please let us know if you would like
9731 another third party package to be included. </span></span></span></span></p>
9733 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc102494674'><span
9734 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc101065205'><span
9735 lang=AF>Whenver on-demand installation or automated installation fails because
9736 of unforessen system specificities, users should install the third party package
9737 manually. This documentation gives some tips we have found useful, but users
9738 are encouraged to check the original documentation.</span></span></span></span></p>
9740 <h2><span style='mso-bookmark:_Toc102494674'><span style='mso-bookmark:_Toc102494294'><span
9741 style='mso-bookmark:_Toc101065205'><a name="_Toc151732198">Standard
9742 Installation</a></span></span></span><span style='mso-bookmark:_Toc151732198'>
9743 of T-Coffee</span></h2>
9745 <h3><a name="_Toc151732199"><span style='mso-hansi-font-family:"Arial Black"'>Automated
9746 Installation</span></a><span style='mso-hansi-font-family:"Arial Black"'><o:p></o:p></span></h3>
9748 <p class=MyNormaBoldl><span lang=AF>We now recommend that you use the automated
9749 installer provided for UNIX or Linux platforms. </span></p>
9751 <h4><a name="_Toc151732200"><span lang=AF>Mac-OsX</span></a></h4>
9753 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9754 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9755 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9756 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9758 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9759 style='mso-tab-count:1'> </span>Click on tge .dmg file</p>
9763 <h4><a name="_Toc151732201"><span lang=AF>Unix</span></a></h4>
9765 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9766 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9767 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9768 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9770 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9771 style='mso-tab-count:1'> </span>rpm –i <rmp></p>
9775 <p class=MsoNormal><o:p> </o:p></p>
9777 <p class=MsoNormal><o:p> </o:p></p>
9779 <p class=MsoNormal><o:p> </o:p></p>
9781 <p class=MsoNormal><o:p> </o:p></p>
9783 <h3><a name="_Toc151732202"><span style='mso-hansi-font-family:"Arial Black"'>Unix</span></a></h3>
9785 <p class=MyNormaBoldl><span lang=AF>You need to have: gcc, g77, CPAN and an
9786 internet connection and your root password. You will also need the two
9787 following perl modules: LWP and XML::Simple. These are needed if you want to
9788 use the web services provided by the EBI via REST (http://www.ebi.ac.uk/Tools/webservices/tutorials/02_rest)</span></p>
9790 <p class=MsoNormal style='margin-left:72.0pt'><o:p> </o:p></p>
9792 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
9793 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
9794 list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
9795 Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>1.<span
9796 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><code><span
9797 style='font-size:10.0pt'>gunzip t_coffee.tar.gz</span></code><span
9798 style='font-family:Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
9800 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
9801 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
9802 list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
9803 Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>2.<span
9804 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><code><span
9805 style='font-size:10.0pt'>tar -xvf t_coffee.tar</span></code><span
9806 style='font-family:Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
9808 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
9809 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
9810 list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
9811 Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>3.<span
9812 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><code><span
9813 style='font-size:10.0pt'>cd t_coffee</span></code><span style='font-family:
9814 Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
9816 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
9817 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
9818 list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
9819 Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>4.<span
9820 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><code><span
9821 style='font-size:10.0pt'>./install t_coffee</span></code><span
9822 style='font-family:Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
9824 <p class=MyNormal><span lang=AF>This installation will only install the stand
9825 alone T-Coffee. If you want to install a specific mode of T-Coffee, you may try
9826 the following commands that will try to gather all the necessary third party
9827 packages. Note that a package already found on your system will not be
9828 re-installed.</span></p>
9830 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9831 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9832 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9833 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9835 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9836 style='mso-tab-count:1'> </span>./install t_coffee</p>
9838 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9839 style='mso-tab-count:1'> </span>./install mcoffee</p>
9841 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9842 style='mso-tab-count:1'> </span>./install 3dcoffee</p>
9844 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9845 style='mso-tab-count:1'> </span>./install rcoffee</p>
9847 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9848 style='mso-tab-count:1'> </span>./install psicoffee</p>
9850 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><o:p> </o:p></p>
9854 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9856 <p class=MyNormal><span lang=AF>Or even</span></p>
9858 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9859 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9860 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9861 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9863 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9864 style='mso-tab-count:1'> </span>./install all</p>
9868 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9870 <p class=MyNormal><span lang=AF>-All the corresponding executables will be
9871 downloaded automatically and installed in</span></p>
9873 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9874 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9875 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9876 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9878 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9879 style='mso-tab-count:1'> </span>$HOME/.t_coffee/plugins</p>
9883 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9885 <p class=MyNormal><span lang=AF>-if you executables are in a different location,
9886 give it to T-Coffee using the -plugins flag.</span></p>
9888 <p class=MyNormal><span lang=AF>-If the installation of any of the companion
9889 package fails, you should install it yourself using the provided link (see
9890 below) and following the authors instructions.<span style='mso-tab-count:1'> </span></span></p>
9892 <p class=MyNormal><span lang=AF>-If you have not managed to install SOAP::Lite,
9893 you can re-install it later (from anywhere) following steps 1-2.</span></p>
9895 <p class=MsoNormal style='margin-left:72.0pt'><o:p> </o:p></p>
9897 <p class=MyNormaBoldl><span lang=AF>-This procedure attempts 3 things:
9898 installing and Compiling T-Coffee (C program), Installing and compiling <a
9899 href="http://zhang.bioinformatics.ku.edu/TM-align/"><span lang=EN-US
9900 style='mso-ansi-language:EN-US'>TMalign</span></a> (Fortran), Installing and
9901 compiling XML::Simple</span></p>
9903 <p class=MyNormaBoldl><span lang=AF><o:p> </o:p></span></p>
9905 <p class=MyNormaBoldl><span lang=AF>-If you have never installed a perl module
9906 before, CPAN will ask you many questions: say Yes to all </span></p>
9908 <p class=MyNormaBoldl><span lang=AF>-If everything went well, the procedure has
9909 created in the <b>bin</b> directory two executables: t_coffee and TMalign (<b>Make
9910 sure these executables are on your $PATH!</b>)</span></p>
9912 <p class=MyNormaBoldl><span lang=AF><o:p> </o:p></span></p>
9914 <h3><a name="_Toc151732203">Microsoft Windows/Cygwin</a></h3>
9916 <p class=MyNormaBoldl><span lang=AF>Install <a href="http://www.cygwin.com"><span
9917 lang=EN-US style='color:windowtext;mso-ansi-language:EN-US;text-decoration:
9918 none;text-underline:none'>Cygwin</span></a></span></p>
9920 <p class=MyNormaBoldl><span lang=AF>Download The Installer (NOT Cygwin/X)</span></p>
9922 <p class=MyNormaBoldl><span lang=AF>Click on view to list ALL the packages</span></p>
9924 <p class=MyNormaBoldl><span lang=AF>Select: gcc-core, make, wget</span></p>
9926 <p class=MyNormaBoldl><span lang=AF>Optional: ssh, xemacs, nano</span></p>
9928 <p class=MyNormaBoldl><span lang=AF>Run mkpasswd in Cywin (as requested when
9929 you start cygwin)</span></p>
9931 <p class=MyNormaBoldl><span lang=AF>Install T-Coffee within Cygwin using the
9932 Unix procedure</span></p>
9934 <h3><a name="_Toc151732204">MAC osX, Linux</a></h3>
9936 <p class=MyNormaBoldl><span lang=AF>Make sure you have the Developer's kit installed
9937 (compilers and makefile)</span></p>
9939 <p class=MyNormaBoldl><span lang=AF>Follow the Unix Procedure</span></p>
9941 <p class=Mylist><span lang=AF><o:p> </o:p></span></p>
9943 <h3><a name="_Toc151732205">CLUSTER Installation</a></h3>
9945 <p class=MyNormal><span lang=AF>In order to run, T-Coffee must have a value for
9946 the http_proxy and for the E-mail. In order to do so you can either:</span></p>
9948 <p class=MyNormaBoldl><span lang=AF>export the following values:</span></p>
9950 <p class=MyNormaBoldl><span lang=AF>export
9951 http_proxy_4_TCOFFEE="proxy" or "" if no proxy</span></p>
9953 <p class=MyNormaBoldl><span lang=AF>export EMAIL_4_TCOFFEE="your
9954 email"</span></p>
9956 <p class=MyNormaBoldl><span lang=AF>OR </span></p>
9958 <p class=MyNormaBoldl><span lang=AF>modify the file ~/.t_coffee/t_coffee_env</span></p>
9960 <p class=MyNormaBoldl><span lang=AF>OR</span></p>
9962 <p class=MyNormaBoldl><span lang=AF>add to your command line: t_coffee
\85.
9963 -proxy=<proxy> -email=<email</span></p>
9965 <p class=MyNormaBoldl><span lang=AF>if you have no proxy: t_coffee
\85 -proxy
9966 -email=<email></span></p>
9968 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
9970 <p class=MsoNormal><o:p> </o:p></p>
9972 <h3><a name="_Toc151732206">If you have PDB installed:</a></h3>
9974 <p class=MyNormal><span lang=AF>Assuming you have a standard PDB installation
9975 in your file system</span></p>
9977 <p class=example2CxSpFirst>setenv (or export)<span style="mso-spacerun:
9978 yes"> </span>PDB_DIR <abs path>/data/structures/all/pdb/</p>
9980 <p class=example2CxSpMiddle>OR</p>
9982 <p class=example2CxSpLast>setenv (or export)<span style="mso-spacerun:
9983 yes"> </span>PDB_DIR <abs path>/structures/divided/pdb/</p>
9985 <p class=MyNormal><span lang=AF>If you do not have PDB installed, don't worry,
9986 t_coffee will go and fetch any structure it needs directly from the PDB
9987 repository. It will simply be a bit slower than if you had PDB locally. </span></p>
9989 <h2><a name="_Toc101065206"></a><a name="_Toc102494295"></a><a
9990 name="_Toc102494675"></a><a name="_Toc151732207"><span style='mso-bookmark:
9991 _Toc102494675'><span style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:
9992 _Toc101065206'>Installing BLAST for T-Coffee</span></span></span></a><span
9993 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
9994 style='mso-bookmark:_Toc101065206'></span></span></span></h2>
9996 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
9997 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
9998 lang=AF>BLAST is a program that search sequence databases for homologues of a
9999 query sequence. It works for proteins and Nucleic Acids. In theory BLAST is
10000 just a package like any, but in practice things are a bit more complex. To run
10001 well, BLST requires up to date databases (that can be fairly large, like NR or
10002 UNIPROT) and a powerful computer.</span></span></span></span></p>
10004 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10005 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10006 lang=AF>Fortunately, an increasing number of institutes or companies are now
10007 providing BLAST clients that run over the net. It means that all you need is a
10008 small program that send your query to the big server and gets the results back.
10009 This prevents you from the hassle of installing and maintaining BLAST, but of
10010 course it is less private and you rely on the network and the current load of
10011 these busy servers.</span></span></span></span></p>
10013 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10014 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10015 lang=AF>Thanks to its interaction with BLAST, T-Coffee can gather structures
10016 and protein profiles and deliver an alignment significantly more accurate than
10017 the default you would get with T-Coffee or any similar method.</span></span></span></span></p>
10019 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10020 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10021 lang=AF>Let us go through the various modes available for T-Coffee</span></span></span></span></p>
10023 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10024 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10025 lang=AF><o:p> </o:p></span></span></span></span></p>
10027 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10028 style='mso-bookmark:_Toc101065206'><a name="_Toc151732208">Why Do I need BLAST
10029 with T-Coffee?</a></span></span></span></h3>
10031 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10032 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10033 lang=AF>The most accurate modes of T-Coffe scan the databases for templates
10034 that they use to align the sequences. There are currently two types of templates
10035 for proteins:</span></span></span></span></p>
10037 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10038 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10039 lang=AF>structures (PDB) that can be found by a blastp against the PDB database
10040 and profiles that can be constructed with eiether a blastp or a psiblast
10041 against nr or uniprot.</span></span></span></span></p>
10043 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10044 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10045 lang=AF>These templates are automatically built if you use:</span></span></span></span></p>
10047 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10048 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10049 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10050 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10052 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10053 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10054 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>t_coffee
10055 <yourseq> -mode expresso</span></span></span></p>
10059 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10060 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10061 lang=AF><span style='mso-tab-count:1'> </span>that
10062 fetches aand uses pdb templates, or</span></span></span></span></p>
10064 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10065 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10066 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10067 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10069 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10070 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10071 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span><span
10072 style='mso-tab-count:1'> </span>t_coffee
10073 <your seq> -mode psicoffee</span></span></span></p>
10077 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10078 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10079 lang=AF><span style='mso-tab-count:1'> </span>that
10080 fetches and uses profile templates, or</span></span></span></span></p>
10082 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10083 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10084 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10085 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10087 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10088 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10089 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span><span
10090 style='mso-tab-count:1'> </span>t_coffee
10091 <your seq> -mode accurate</span></span></span></p>
10095 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10096 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10097 lang=AF><span style='mso-tab-count:1'> </span>that
10098 does everything and tries to use the best template. Now that you see why it is
10099 useful let's see how to get BLAST up and running, from the easy solution to
10100 tailor made ones.</span></span></span></span></p>
10102 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10103 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10104 lang=AF><o:p> </o:p></span></span></span></span></p>
10106 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10107 style='mso-bookmark:_Toc101065206'><a name="_Toc151732209">Using the EBI BLAST
10108 Client</a></span></span></span></h3>
10110 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10111 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10112 lang=AF>This is by far the easiest (and the default mode). The perl clients are
10113 already incorporated in T-Coffee and all you need is are the proper perl
10114 library. In theory, T-Coffee should have already installed these libraries during
10115 the standard installation. Yet, this requires having toot access. It really is
10116 worth the effort, since the EBI is providing one of the best webservice available
10117 around, and most notably, the only public psiblast via a web service.</span></span></span></span></p>
10119 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10120 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10121 lang=AF>Whenever you use a T-Coffee mode requiring Blast access, it will ask
10122 you for an authentification E-mail. <b>Be Careful! </b>If you provide a fake
10123 E-mail, the EBI may suspend the service for all machines associated with your
10124 IP address (that could mean your entire lab, or entire institute, or even the
10125 entire country or, but I doubt it, the whole universe).</span></span></span></span></p>
10127 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10128 style='mso-bookmark:_Toc101065206'><a name="_Toc151732210">Using the NCBI BLAST
10129 Client</a></span></span></span></h3>
10131 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10132 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10133 lang=AF>The NCBI is the next best alternative. In my hand it was always a bit
10134 slower and most of all, it does not incorporate PSI-BLAST (as a web sevice). A
10135 big miss. The NCBI web blast client is a small executable that you should
10136 install on your system following the instructions given on this link</span></span></span></span></p>
10138 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10139 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10140 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10141 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10143 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10144 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10145 style='mso-bookmark:_Toc101065206'>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></p>
10149 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10150 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10151 lang=AF>Simply go for <b>netbl,</b> download the executable that corresponds to
10152 your architecture (cygwin users should go for the win executable). Despite all
10153 the files that come along the executable blastcl3 is a stand alone executable
10154 that you can safely move to your $BIN.</span></span></span></span></p>
10156 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10157 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10158 lang=AF>All you will then need to do is to make sure that T-Coffee uses the
10159 right client, when you run it.</span></span></span></span></p>
10161 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10162 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10163 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10164 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10166 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10167 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10168 style='mso-bookmark:_Toc101065206'>-blast_server=NCBI</span></span></span></p>
10172 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10173 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10174 lang=AF>No need for any E-mail here, but you don't get psiblast, and whenever
10175 T-Coffee wants to use it, blastp will be used instead.</span></span></span></span></p>
10177 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10178 style='mso-bookmark:_Toc101065206'><a name="_Toc151732211">Using another Client</a></span></span></span></h3>
10180 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10181 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10182 lang=AF>You may have your own client (lucky you). If that is so, all you need
10183 is to make sure that this client is complient with the blast command line. If
10184 your client is named foo.pl, all you need to to is run T-Coffee with</span></span></span></span></p>
10186 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10187 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10188 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10189 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10191 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10192 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10193 style='mso-bookmark:_Toc101065206'>-blast_server=CLIENT_foo.pl</span></span></span></p>
10197 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10198 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10199 lang=AF>Foo will be called as if it were blastpgp, and it is your
10200 responsability to make sure it can handle the following command line:</span></span></span></span></p>
10202 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10203 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10204 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10205 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10207 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10208 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10209 style='mso-bookmark:_Toc101065206'>foo.pl -p <method> -d <db> -i <infile>
10210 -o <outfile> -m 7</span></span></span></p>
10214 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10215 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10216 lang=AF>method can either be blastp or psiblast.</span></span></span></span></p>
10218 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10219 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10220 lang=AF>infile is a FASTA file</span></span></span></span></p>
10222 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10223 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10224 lang=AF>-m7 triggers the XML output. T-Coffee is able to parse both the EBI XML
10225 output and the NCBI XML output.</span></span></span></span></p>
10227 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10228 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10229 lang=AF><o:p> </o:p></span></span></span></span></p>
10231 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10232 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10233 lang=AF>If foo.pl behaves differently, the easiest will probably be to write a
10234 wrapper around it so that wrapped_foo.pl behaves like blastpgp</span></span></span></span></p>
10236 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10237 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10238 lang=AF><o:p> </o:p></span></span></span></span></p>
10240 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10241 style='mso-bookmark:_Toc101065206'><a name="_Toc151732212">Using a BLAST local
10242 version on UNIX</a></span></span></span></h3>
10244 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10245 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10246 lang=AF>If you have blastpgp installed, you can run it instead of the remote
10247 clients by using:</span></span></span></span></p>
10249 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10250 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10251 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10252 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10254 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10255 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10256 style='mso-bookmark:_Toc101065206'>-blast_server=LOCAL</span></span></span></p>
10260 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10261 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10262 lang=AF><span style="mso-spacerun: yes"> </span>The documentation for
10263 blastpgp can be found on:</span></span></span></span></p>
10265 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10266 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10267 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10268 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10270 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10271 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10272 style='mso-bookmark:_Toc101065206'>www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastpgp.html</span></span></span></p>
10276 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10277 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10278 lang=AF>and the package is part of the standard BLAST distribution</span></span></span></span></p>
10280 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10281 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10282 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10283 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10285 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10286 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10287 style='mso-bookmark:_Toc101065206'>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></p>
10291 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10292 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10293 lang=AF>Depending on your system, your own skills, your requirements and on
10294 more parameters than I have fingers to count, installing a BLAST server suited
10295 for your needs can range from a 10 minutes job to an achivement spread over
10296 several generations. So at this point, you should roam the NCBI website for
10297 suitable information.</span></span></span></span></p>
10299 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10300 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10301 lang=AF>If you want to have your own BLAST server to run your own databases,
10302 you should know that it is possible to control both the database and the
10303 program used by BLAST:</span></span></span></span></p>
10305 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10306 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10307 lang=AF><o:p> </o:p></span></span></span></span></p>
10309 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
10310 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
10311 background:#E6E6E6'>
10313 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
10314 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-protein_db:
10315 will specify the database used by all the psi-blast modes</span></span></span></p>
10317 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
10318 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-pdb_db:
10319 will specify the database used by the pdb modes</span></span></span></p>
10323 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10324 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><b
10325 style='mso-bidi-font-weight:normal'><span lang=AF><o:p> </o:p></span></b></span></span></span></p>
10327 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
10328 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
10330 <p class=Warning><span style='mso-bookmark:_Toc102494675'><span
10331 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Note
10332 that T-Coffee is compliant with BLAST+, the latest NCBI Blast.</span></span></span></p>
10336 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10337 style='mso-bookmark:_Toc101065206'><a name="_Toc151732213">Using a BLAST local
10338 version on Windows/cygwin</a></span></span></span></h3>
10340 <h4><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10341 style='mso-bookmark:_Toc101065206'><a name="_Toc151732214"><span lang=AF>BLAST+</span></a></span></span></span></h4>
10343 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10344 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10345 lang=AF>Blast+ is tghe latest NCBI Blast. IT is easier to install. A default
10346 installation should be compliant with a default T-Coffee installation. </span></span></span></span></p>
10348 <p class=MsoNormal><span style='mso-bookmark:_Toc102494675'><span
10349 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p> </o:p></span></span></span></p>
10351 <h4><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10352 style='mso-bookmark:_Toc101065206'><a name="_Toc151732215"><span lang=AF>ORIGINAL
10353 NCBI BLAST</span></a></span></span></span></h4>
10355 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10356 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10357 lang=AF>For those of you using cygwin, be careful. While cygwin behaves like a
10358 UNIX system, the BLAST executable required for cygwin (win32) is expecting
10359 WINDOWS path and not UNIX path. This has three important consequences:</span></span></span></span></p>
10361 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10362 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10363 lang=AF>1- the ncbi file declaring the Data directory must be:</span></span></span></span></p>
10365 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10366 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10367 lang=AF><span style='mso-tab-count:1'> </span>C:WINDOWS//ncbi.init<span
10368 style="mso-spacerun: yes"> </span>[at the root of your WINDOWS]</span></span></span></span></p>
10370 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10371 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10372 lang=AF>2- the address mentionned with this file must be WINDOWS formated, for
10373 instance, on my system:</span></span></span></span></p>
10375 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10376 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10377 lang=AF>Data=C:\cygwin\home\notredame\blast\data</span></span></span></span></p>
10379 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10380 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10381 lang=AF>3- When you pass database addresses to BLAST, these must be in Windows format:</span></span></span></span></p>
10383 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10384 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10385 lang=AF><span style='mso-tab-count:1'> </span>-protein_db="c:/somewhere/somewhereelse/database"</span></span></span></span></p>
10387 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10388 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10389 lang=AF>(using the slash (/) or the andtislash (\) does not matter on new
10390 systems but I would reommand against incorporating white spaces.</span></span></span></span></p>
10392 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10393 style='mso-bookmark:_Toc101065206'><a name="_Toc151732216">Installing Other
10394 Companion Packages</a></span></span></span></h2>
10396 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10397 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10398 lang=AF>T-Coffee is meant to interact with as many packages as possible, either
10399 for aligning or using predictions. If you type </span></span></span></span></p>
10401 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10402 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10403 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10404 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10406 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10407 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10408 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>t_coffee</span></span></span></p>
10412 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10413 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10414 lang=AF>You will receive a list of supported packages that looks like the next
10415 table. In theory, most of these packages can be installed by T-Coffee <b
10416 style='mso-bidi-font-weight:normal'>and we welcome any reasonnable request.<o:p></o:p></b></span></span></span></span></p>
10418 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10419 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10420 lang=AF><o:p> </o:p></span></span></span></span></p>
10422 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
10423 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
10424 background:#E6E6E6'>
10426 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
10427 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>******
10428 Pairwise Sequence Alignment Methods:</span></span></span></p>
10430 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10431 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>--------------------------------------------</span></span></span></p>
10433 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10434 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>fast_pair<span
10435 style="mso-spacerun:
10436 yes"> </span>built_in</span></span></span></p>
10438 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10439 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>exon3_pair<span
10440 style="mso-spacerun: yes">
10441 </span>built_in</span></span></span></p>
10443 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10444 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>exon2_pair<span
10445 style="mso-spacerun: yes">
10446 </span>built_in</span></span></span></p>
10448 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10449 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>exon_pair<span
10450 style="mso-spacerun:
10451 yes"> </span>built_in</span></span></span></p>
10453 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10454 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>slow_pair<span
10455 style="mso-spacerun:
10456 yes"> </span>built_in</span></span></span></p>
10458 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10459 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proba_pair<span
10460 style="mso-spacerun: yes">
10461 </span>built_in</span></span></span></p>
10463 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10464 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>lalign_id_pair<span
10465 style="mso-spacerun: yes"> </span>built_in</span></span></span></p>
10467 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10468 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>seq_pair<span
10469 style="mso-spacerun:
10470 yes">
10471 </span>built_in</span></span></span></p>
10473 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10474 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>externprofile_pair
10475 built_in</span></span></span></p>
10477 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10478 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>hh_pair<span
10479 style="mso-spacerun:
10480 yes">
10481 </span>built_in</span></span></span></p>
10483 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10484 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>profile_pair<span
10485 style="mso-spacerun: yes"> </span>built_in</span></span></span></p>
10487 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10488 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>cdna_fast_pair<span
10489 style="mso-spacerun: yes"> </span>built_in</span></span></span></p>
10491 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10492 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>cdna_cfast_pair<span
10493 style="mso-spacerun: yes"> </span>built_in</span></span></span></p>
10495 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10496 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>clustalw_pair<span
10497 style="mso-spacerun: yes"> </span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></p>
10499 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10500 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafft_pair<span
10501 style="mso-spacerun: yes">
10502 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10504 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10505 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftjtt_pair<span
10506 style="mso-spacerun: yes">
10507 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10509 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10510 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftgins_pair<span
10511 style="mso-spacerun: yes">
10512 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10514 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10515 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialigntx_pair<span
10516 style="mso-spacerun: yes">
10517 </span>http://dialign-tx.gobics.de/</span></span></span></p>
10519 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10520 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialignt_pair<span
10521 style="mso-spacerun: yes">
10522 </span>http://dialign-t.gobics.de/</span></span></span></p>
10524 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10525 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>poa_pair<span
10526 style="mso-spacerun:
10527 yes">
10528 </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></p>
10530 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10531 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>probcons_pair<span
10532 style="mso-spacerun: yes">
10533 </span>http://probcons.stanford.edu/</span></span></span></p>
10535 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10536 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>muscle_pair<span
10537 style="mso-spacerun: yes">
10538 </span>http://www.drive5.com/muscle/</span></span></span></p>
10540 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10541 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>t_coffee_pair<span
10542 style="mso-spacerun: yes">
10543 </span>http://www.tcoffee.org</span></span></span></p>
10545 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10546 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>pcma_pair<span
10547 style="mso-spacerun:
10548 yes">
10549 </span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></p>
10551 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10552 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>kalign_pair<span
10553 style="mso-spacerun: yes">
10554 </span>http://msa.cgb.ki.se</span></span></span></p>
10556 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10557 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>amap_pair<span
10558 style="mso-spacerun:
10559 yes">
10560 </span>http://bio.math.berkeley.edu/amap/</span></span></span></p>
10562 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10563 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proda_pair<span
10564 style="mso-spacerun: yes">
10565 </span>http://bio.math.berkeley.edu/proda/</span></span></span></p>
10567 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10568 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>prank_pair<span
10569 style="mso-spacerun: yes"> </span><span style="mso-spacerun:
10570 yes"> </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></p>
10572 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10573 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>consan_pair<span
10574 style="mso-spacerun: yes">
10575 </span>http://selab.janelia.org/software/consan/</span></span></span></p>
10577 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10578 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p> </o:p></span></span></span></p>
10580 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10581 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>******
10582 Pairwise Structural Alignment Methods:</span></span></span></p>
10584 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10585 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>--------------------------------------------</span></span></span></p>
10587 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10588 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>align_pdbpair<span
10589 style="mso-spacerun: yes"> </span>built_in</span></span></span></p>
10591 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10592 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>lalign_pdbpair<span
10593 style="mso-spacerun: yes"> </span>built_in</span></span></span></p>
10595 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10596 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>extern_pdbpair<span
10597 style="mso-spacerun: yes"> </span>built_in</span></span></span></p>
10599 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10600 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>thread_pair<span
10601 style="mso-spacerun: yes">
10602 </span>built_in</span></span></span></p>
10604 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10605 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>fugue_pair<span
10606 style="mso-spacerun: yes">
10607 </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></p>
10609 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10610 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>pdb_pair<span
10611 style="mso-spacerun:
10612 yes">
10613 </span>built_in</span></span></span></p>
10615 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10616 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>sap_pair<span
10617 style="mso-spacerun:
10618 yes">
10619 </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></p>
10621 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10622 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mustang_pair<span
10623 style="mso-spacerun: yes">
10624 </span>http://www.cs.mu.oz.au/~arun/mustang/</span></span></span></p>
10626 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10627 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>tmalign_pair<span
10628 style="mso-spacerun: yes">
10629 </span>http://zhang.bioinformatics.ku.edu/TM-align/</span></span></span></p>
10631 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10632 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p> </o:p></span></span></span></p>
10634 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10635 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>******
10636 Multiple Sequence Alignment Methods:</span></span></span></p>
10638 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10639 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>--------------------------------------------</span></span></span></p>
10641 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10642 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>clustalw_msa<span
10643 style="mso-spacerun: yes">
10644 </span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></p>
10646 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10647 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafft_msa<span
10648 style="mso-spacerun:
10649 yes"> </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10651 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10652 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftjtt_msa<span
10653 style="mso-spacerun: yes">
10654 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10656 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10657 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftgins_msa<span
10658 style="mso-spacerun: yes">
10659 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10661 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10662 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialigntx_msa<span
10663 style="mso-spacerun: yes">
10664 </span>http://dialign-tx.gobics.de/</span></span></span></p>
10666 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10667 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialignt_msa<span
10668 style="mso-spacerun: yes">
10669 </span>http://dialign-t.gobics.de/</span></span></span></p>
10671 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10672 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>poa_msa<span
10673 style="mso-spacerun:
10674 yes">
10675 </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></p>
10677 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10678 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>probcons_msa<span
10679 style="mso-spacerun: yes">
10680 </span>http://probcons.stanford.edu/</span></span></span></p>
10682 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10683 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>muscle_msa<span
10684 style="mso-spacerun: yes">
10685 </span>http://www.drive5.com/muscle/</span></span></span></p>
10687 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10688 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>t_coffee_msa<span
10689 style="mso-spacerun: yes">
10690 </span>http://www.tcoffee.org</span></span></span></p>
10692 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10693 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>pcma_msa<span
10694 style="mso-spacerun:
10695 yes">
10696 </span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></p>
10698 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10699 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>kalign_msa<span
10700 style="mso-spacerun: yes">
10701 </span>http://msa.cgb.ki.se</span></span></span></p>
10703 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10704 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>amap_msa<span
10705 style="mso-spacerun:
10706 yes">
10707 </span>http://bio.math.berkeley.edu/amap/</span></span></span></p>
10709 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10710 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proda_msa<span
10711 style="mso-spacerun:
10712 yes">
10713 </span>http://bio.math.berkeley.edu/proda/</span></span></span></p>
10715 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10716 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>prank_msa<span
10717 style="mso-spacerun:
10718 yes">
10719 </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></p>
10721 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10722 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p> </o:p></span></span></span></p>
10724 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10725 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>#######<span
10726 style="mso-spacerun: yes"> </span>Prediction Methods available to
10727 generate Templates</span></span></span></p>
10729 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10730 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-------------------------------------------------------------</span></span></span></p>
10732 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10733 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>RNAplfold<span
10734 style="mso-spacerun:
10735 yes">
10736 </span>http://www.tbi.univie.ac.at/~ivo/RNA/</span></span></span></p>
10738 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10739 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>HMMtop<span
10740 style="mso-spacerun:
10741 yes">
10742 </span>www.enzim.hu/hmmtop/</span></span></span></p>
10744 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10745 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>GOR4<span
10746 style="mso-spacerun:
10747 yes">
10748 </span>http://mig.jouy.inra.fr/logiciels/gorIV/</span></span></span></p>
10750 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10751 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>wublast_client<span
10752 style="mso-spacerun: yes">
10753 </span>http://www.ebi.ac.uk/Tools/webservices/services/wublast</span></span></span></p>
10755 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10756 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>blastpgp_client<span
10757 style="mso-spacerun: yes">
10758 </span>http://www.ebi.ac.uk/Tools/webservices/services/blastpgp<span
10759 style="mso-spacerun:
10760 yes"> </span></span></span></span></p>
10762 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
10763 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>==========================================================</span></span></span></p>
10767 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10768 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10769 lang=AF><o:p> </o:p></span></span></span></span></p>
10771 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10772 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10773 lang=AF><o:p> </o:p></span></span></span></span></p>
10775 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10776 style='mso-bookmark:_Toc101065206'><a name="_Toc151732217">Installation of
10777 PSI-Coffee and Expresso</a></span></span></span></h2>
10779 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10780 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10781 lang=AF>PSI-Coffee is a mode of T-Coffee that runs a a Psi-BLAST on each of
10782 your sequences and makes a multiple profile alignment. If you do not have any
10783 structural information, it is by far the most accurate mode of T-Coffee. To use
10784 it, you must have SOAP installed so that the EBI BLAST client can run on your
10785 system.</span></span></span></span></p>
10787 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10788 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10789 lang=AF>It is a bit slow, but really worth it if your sequences are hard to
10790 align and if the accuracy of your alignment is important.<span
10791 style="mso-spacerun: yes"> </span></span></span></span></span></p>
10793 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10794 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10795 lang=AF>To use this mode, try:</span></span></span></span></p>
10797 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10798 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10799 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10800 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10802 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10803 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10804 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>t_coffee
10805 <yoursequence> -mode psicoffee</span></span></span></p>
10809 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10810 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10811 lang=AF>Note that because PSI-BLAST is time consuming, T-Coffee stores the runs
10812 in its cache (./tcoffee/cache) so that it does not need to be re-run. It means
10813 that if you re-align your sequences (or add a few extra sequences), things will
10814 be considerably faster.</span></span></span></span></p>
10816 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10817 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10818 lang=AF>If your installation procedure has managed to compile TMalign, and if
10819 T-Coffee has access to the EBI BLAST server (or any other server) you can also
10820 do the following:</span></span></span></span></p>
10822 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10823 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10824 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10825 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10827 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10828 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10829 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>t_coffee
10830 <yoursequence> -mode expresso</span></span></span></p>
10834 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10835 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10836 lang=AF>That will look for structural templates. And if both these modes are
10837 running fine, then you are ready for the best, the "crème de la
10838 crème":</span></span></span></span></p>
10840 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10841 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10842 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10843 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10845 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10846 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10847 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>t_coffee
10848 <yoursequence> -mode accurate</span></span></span></p>
10852 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10853 style='mso-bookmark:_Toc101065206'><a name="_Toc151732218">Installation of
10854 M-Coffee</a></span></span></span></h2>
10856 <p class=MsoNormal><span style='mso-bookmark:_Toc102494675'><span
10857 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p> </o:p></span></span></span></p>
10859 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10860 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10861 lang=AF>M-Coffee is a special mode of T-Coffee that makes it possible to combine
10862 the output of many multiple sequence alignment packages. </span></span></span></span><span
10863 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10864 style='mso-bookmark:_Toc101065206'><span style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></p>
10866 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10867 style='mso-bookmark:_Toc101065206'><a name="_Toc151732219">Automated
10868 Installation</a></span></span></span></h3>
10870 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10871 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10872 lang=AF>In the T-Coffee distribution, type:</span></span></span></span></p>
10874 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10875 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10876 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10877 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10879 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10880 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10881 style='mso-bookmark:_Toc101065206'>./install mcoffee</span></span></span></p>
10885 <p class=MsoNormal><span style='mso-bookmark:_Toc102494675'><span
10886 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p> </o:p></span></span></span></p>
10888 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10889 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10890 lang=AF>In theory, this command should download and install every required
10891 package. If, however, it fails, you should switch to the manual installation
10892 (see next).</span></span></span></span></p>
10894 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10895 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10896 lang=AF>By default these packages will be in </span></span></span></span></p>
10898 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10899 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10900 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10901 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10903 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10904 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10905 style='mso-bookmark:_Toc101065206'>$HOME/.t_coffee/plugins</span></span></span></p>
10909 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10910 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10911 lang=AF>If you want to have these companion packages in a different directory,
10912 you can either set the environement variable </span></span></span></span></p>
10914 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10915 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10916 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10917 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10919 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10920 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10921 style='mso-bookmark:_Toc101065206'>setenv PLUGINS_4_TCOFFEE=<plugins dir></span></span></span></p>
10925 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10926 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10927 lang=AF>Or use the command line flag -plugin (over-rides every other setting)</span></span></span></span></p>
10929 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10930 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10931 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10932 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10934 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10935 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10936 style='mso-bookmark:_Toc101065206'>t_coffee ... -plugins=<plugins dir></span></span></span></p>
10940 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10941 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10942 lang=AF><o:p> </o:p></span></span></span></span></p>
10944 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10945 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10946 lang=AF><o:p> </o:p></span></span></span></span></p>
10948 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10949 style='mso-bookmark:_Toc101065206'><a name="_Toc151732220">Manual Installation</a></span></span></span></h3>
10951 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10952 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10953 lang=AF>M-Coffee requires a standard T-Coffee installation (c.f. previous
10954 section) and the following packages to be installed on your system:</span></span></span></span></p>
10956 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10957 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10958 lang=AF><span style='mso-tab-count:1'> </span></span></span></span></span></p>
10960 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
10961 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
10962 background:#E6E6E6'>
10964 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
10965 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Package<span
10966 style='mso-tab-count:2'> </span>Where
10967 From</span></span></span></p>
10969 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10970 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>==========================================================</span></span></span></p>
10972 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10973 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ClustalW<span
10974 style='mso-tab-count:2'> </span>can
10975 interact with t_coffee</span></span></span></p>
10977 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10978 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
10980 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10981 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Poa<span
10982 style='mso-tab-count:3'> </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></p>
10984 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10985 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
10987 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10988 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Muscle<span
10989 style='mso-tab-count:2'> </span>http://www.drive5.com</span></span></span></p>
10991 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10992 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10993 style="mso-spacerun:
10994 yes"> </span>----------------------------------------------------------</span></span></span></p>
10996 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10997 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ProbCons<span
10998 style='mso-tab-count:2'> </span>http://probcons.stanford.edu/</span></span></span></p>
11000 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11001 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ProbConsRNA<span
11002 style='mso-tab-count:2'> </span>http://probcons.stanford.edu/</span></span></span></p>
11004 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11005 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11007 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11008 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>MAFFT<span
11009 style='mso-tab-count:1'> </span></span></span></span><a
11010 href="http://www.biophys.kyoto-/"><span style='mso-bookmark:_Toc102494675'><span
11011 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>http://www.biophys.kyoto-</span></span></span><span
11012 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11013 style='mso-bookmark:_Toc101065206'></span></span></span></a><span
11014 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11015 style='mso-bookmark:_Toc101065206'>u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
11017 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11018 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11020 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11021 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Dialign-T<span
11022 style='mso-tab-count:2'> </span></span></span></span><a
11023 href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc102494675'><span
11024 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>http://dialign-t.gobics.de/</span></span></span><span
11025 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11026 style='mso-bookmark:_Toc101065206'></span></span></span></a><span
11027 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11028 style='mso-bookmark:_Toc101065206'></span></span></span></p>
11030 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11031 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Dialign-TX<span
11032 style='mso-tab-count:2'> </span></span></span></span><a
11033 href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc102494675'><span
11034 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>http://dialign-tx.gobics.de/</span></span></span><span
11035 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11036 style='mso-bookmark:_Toc101065206'></span></span></span></a><span
11037 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11038 style='mso-bookmark:_Toc101065206'></span></span></span></p>
11040 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11041 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11043 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11044 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>PCMA<span
11045 style='mso-tab-count:3'> </span></span></span></span><a
11046 href="file://localhost/pub/PCMA"><span style='mso-bookmark:_Toc102494675'><span
11047 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ftp://iole.swmed.edu/pub/PCMA/</span></span></span><span
11048 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11049 style='mso-bookmark:_Toc101065206'></span></span></span></a><span
11050 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11051 style='mso-bookmark:_Toc101065206'></span></span></span></p>
11053 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11054 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11056 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11057 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>kalign<span
11058 style="mso-spacerun:
11059 yes">
11060 </span>http://msa.cgb.ki.se</span></span></span></p>
11062 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11063 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11065 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11066 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>amap<span
11067 style="mso-spacerun:
11068 yes">
11069 </span>http://bio.math.berkeley.edu/amap/</span></span></span></p>
11071 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11072 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-----------------------------------------------------------</span></span></span></p>
11074 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11075 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proda_msa<span
11076 style="mso-spacerun: yes">
11077 </span>http://bio.math.berkeley.edu/proda/</span></span></span></p>
11079 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11080 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-----------------------------------------------------------</span></span></span></p>
11082 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11083 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>prank_msa<span
11084 style="mso-spacerun: yes">
11085 </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></p>
11087 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
11088 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p> </o:p></span></span></span></p>
11092 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11093 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11094 lang=AF><o:p> </o:p></span></span></span></span></p>
11096 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11097 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11098 lang=AF>In our hands all these packages where very straightforward to compile
11099 and install on a standard cygwin or Linux configuration. Just make sure you
11100 have gcc, the C compiler, properly installed.</span></span></span></span></p>
11102 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11103 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11104 lang=AF>Once the package is compiled and ready to use, make sure that the
11105 executable is on your path, so that t_coffee can find it automatically. Our
11106 favorite procedure is to create a bin directory in the home. If you do so, make
11107 sure this bin is in your path and fill it with all your executables (this is a
11108 standard Unix practice).</span></span></span></span></p>
11110 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11111 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11112 lang=AF>If for some reason, you do not want this directory to be on your path,
11113 or you want to specify a precise directory containing the executables, you can
11114 use:</span></span></span></span></p>
11116 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11117 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11118 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11119 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11121 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11122 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11123 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>export
11124 PLUGINS_4_TCOFFEE=<dir></span></span></span></p>
11128 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11129 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11130 lang=AF>By default this directory is set to $HOME/.t_coffee/plugins/$OS, but
11131 you can over-ride it with the environement variable or using the flag:</span></span></span></span></p>
11133 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11134 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11135 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11136 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11138 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11139 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11140 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>t_coffee
11141 ...-plugins=<dir></span></span></span></p>
11145 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11146 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11147 lang=AF><o:p> </o:p></span></span></span></span></p>
11149 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11150 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11151 lang=AF>If you cannot, or do not want to use a single bin directory, you can
11152 set the following environment variables to the absolute path values of the
11153 executable you want to use. Whenever they are set, these variables will
11154 supersede any other declaration. This is a convenient way to experiment with
11155 multiple package versions.</span></span></span></span></p>
11157 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11158 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11159 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11160 background:#FFFFCC;margin-left:70.2pt;margin-right:0cm'>
11162 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11163 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11164 style='mso-bookmark:_Toc101065206'>POA_4_TCOOFFEE<br>
11165 CLUSTALW_4_TCOFFEE<br>
11167 TCOFFEE_4_TCOFFEE<br>
11168 MAFFT_4_TCOFFEE<br>
11169 MUSCLE_4_TCOFFEE<br>
11170 DIALIGNT_4_TCOFFEE<br>
11171 PRANK_4_TCOFFEE<br>
11172 DIALIGNTX_4_TCOFFEE<br>
11173 <span style="mso-spacerun: yes"> </span></span></span></span></p>
11177 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11178 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11179 lang=AF>For three of these packages, you will need to copy some of the files in
11180 a special T-Coffee directory.</span></span></span></span></p>
11182 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11183 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11184 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11185 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11187 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11188 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11189 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>cp
11190 POA_DIR/* ~/.t_coffee/mcoffee/</span></span></span></p>
11192 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11193 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11194 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>cp
11195 DIALIGN-T/conf/*<span style="mso-spacerun: yes">
11196 </span>~/.t_coffee/mcoffee</span></span></span></p>
11198 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11199 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11200 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>cp
11201 DIALIGN-TX/conf/*<span style="mso-spacerun: yes">
11202 </span>~/.t_coffee/mcoffee</span></span></span></p>
11206 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11207 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11208 lang=AF>Note that the following files are enough for default usage:</span></span></span></span></p>
11210 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11211 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11212 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11213 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11215 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11216 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11217 style='mso-bookmark:_Toc101065206'>BLOSUM.diag_prob_t10<span
11218 style="mso-spacerun: yes"> </span>BLOSUM75.scr<span
11219 style="mso-spacerun: yes"> </span>blosum80_trunc.mat<span
11220 style="mso-spacerun:
11221 yes"> </span></span></span></span></p>
11223 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11224 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11225 style='mso-bookmark:_Toc101065206'>dna_diag_prob_100_exp_330000<span
11226 style="mso-spacerun: yes"> </span>dna_diag_prob_200_exp_110000</span></span></span></p>
11228 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11229 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11230 style='mso-bookmark:_Toc101065206'>BLOSUM.scr<span style="mso-spacerun:
11231 yes">
11232 </span>BLOSUM90.scr<span style="mso-spacerun: yes">
11233 </span>dna_diag_prob_100_exp_110000</span></span></span></p>
11235 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11236 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11237 style='mso-bookmark:_Toc101065206'>dna_diag_prob_100_exp_550000<span
11238 style="mso-spacerun: yes"> </span>dna_diag_prob_250_exp_110000</span></span></span></p>
11240 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11241 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11242 style='mso-bookmark:_Toc101065206'>BLOSUM75.diag_prob_t2<span
11243 style="mso-spacerun: yes"> </span>blosum80.mat<span style="mso-spacerun:
11244 yes"> </span>dna_diag_prob_100_exp_220000<span style="mso-spacerun:
11245 yes"> </span></span></span></span></p>
11247 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11248 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11249 style='mso-bookmark:_Toc101065206'>dna_diag_prob_150_exp_110000<span
11250 style="mso-spacerun: yes"> </span>dna_matrix.scr</span></span></span></p>
11254 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11255 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11256 lang=AF><o:p> </o:p></span></span></span></span></p>
11258 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11259 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11260 lang=AF>If you would rather have the mcoffee directory in some other location,
11261 set the MCOFFEE_4_TCOFFEE environement variable to the propoer directory:</span></span></span></span></p>
11263 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11264 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11265 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11266 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11268 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11269 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11270 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>setenv
11271 MCOFFEE_4_TCOFFEE <directory containing mcoffee files></span></span></span></p>
11275 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11276 style='mso-bookmark:_Toc101065206'><a name="_Toc151732221">Installation of APDB
11277 and iRMSD</a></span></span></span></h2>
11279 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11280 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>APDB
11281 and iRMSD are incorporated in T-Coffee. Once t_coffee is installed, you can
11282 invoque these programs by typing:</span></span></span></p>
11284 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11285 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11286 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11287 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11289 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11290 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11291 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>t_coffee
11292 –other_pg apdb<br>
11293 <span style='mso-tab-count:1'> </span>t_coffee –other_pg
11294 irmsd</span></span></span></p>
11298 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11299 style='mso-bookmark:_Toc101065206'><a name="_Toc151732222">Installation of tRMSD</a></span></span></span></h2>
11301 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11302 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>tRMSD
11303 comes along with t_coffee but it also requires the package phylip in order to
11304 be functional. Phylip can be obtained from:</span></span></span></p>
11306 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11307 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11308 lang=AF><span style='mso-tab-count:1'> </span></span></span></span></span></p>
11310 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11311 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11312 background:#E6E6E6'>
11314 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
11315 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Package<span
11316 style='mso-tab-count:2'> </span>Function</span></span></span></p>
11318 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11319 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>===================================================</span></span></span></p>
11321 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11322 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>---------------------------------------------------</span></span></span></p>
11324 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11325 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Phylip<span
11326 style='mso-tab-count:2'> </span>Phylogenetic
11327 tree computation</span></span></span></p>
11329 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11330 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11331 style='mso-tab-count:3'> </span>evolution.genetics.washington.edu/phylip.html</span></span></span></p>
11333 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
11334 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>---------------------------------------------------</span></span></span></p>
11338 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11339 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11340 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11341 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11343 <p class=MyExample style='margin-left:0cm;text-indent:14.1pt;background:#FFFFCC'><span
11344 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11345 style='mso-bookmark:_Toc101065206'>t_coffee –other_pg trmsd</span></span></span></p>
11349 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11350 style='mso-bookmark:_Toc101065206'><o:p> </o:p></span></span></span></h2>
11352 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11353 style='mso-bookmark:_Toc101065206'><a name="_Toc151732223">Installation of
11354 seq_reformat</a></span></span></span></h2>
11356 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11357 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Seq_reformat
11358 is a reformatting package that is part of t_coffee. To use it (and see the
11359 available options), type:</span></span></span></p>
11361 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11362 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11363 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11364 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11366 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11367 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11368 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>t_coffee
11369 –other_pg seq_reformat</span></span></span></p>
11373 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11374 style='mso-bookmark:_Toc101065206'><a name="_Toc151732224">Installation of
11375 extract_from_pdb</a></span></span></span></h2>
11377 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11378 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Extract_from_pdb
11379 is a PDB reformatting package that is part of t_coffee. To use it (and see the
11380 available options), type.</span></span></span></p>
11382 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11383 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11384 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11385 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11387 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11388 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11389 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'> </span>t_coffee
11390 –other_pg extract_from_pdb –h</span></span></span></p>
11394 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11395 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Extract_from_pdb
11396 requires wget in order to automatically fetch PDB structures.</span></span></span></p>
11398 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11399 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p> </o:p></span></span></span></p>
11401 <span style='mso-bookmark:_Toc101065206'></span><span style='mso-bookmark:_Toc102494295'></span><span
11402 style='mso-bookmark:_Toc102494675'></span>
11404 <h2><a name="_Toc151732225">Installation of 3D-Coffee/Expresso</a></h2>
11406 <p class=MyNormal><span lang=AF>3D-Coffee/Expresso is a special mode of
11407 T-Coffee that makes it possible to combine sequences and structures. The main
11408 difference between Expresso and 3D-Coffee is that Expresso fetches the
11409 structures itself. </span><span style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
11411 <h3><a name="_Toc151732226">Automated Installation</a></h3>
11413 <p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>
11415 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11416 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11417 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11418 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11420 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>./install
11423 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>OR</p>
11425 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>./install
11430 <p class=MsoNormal><o:p> </o:p></p>
11432 <p class=MyNormal><span lang=AF>In theory, this command should download and
11433 install every required package (<b>except fugue</b>). If, however, it fails,
11434 you should switch to the manual installation (see next).</span></p>
11436 <h3><a name="_Toc151732227">Manual Installation</a></h3>
11438 <p class=MyNormal><span lang=AF>In order to make the most out of T-Coffee, you
11439 will need to install the following packages (make sure the executable is named
11440 as indicated below):</span></p>
11442 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span></span></p>
11444 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11445 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11446 background:#E6E6E6'>
11448 <p class=examplefileCxSpFirst>Package<span style='mso-tab-count:2'> </span>Function</p>
11450 <p class=examplefileCxSpMiddle>===================================================</p>
11452 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11454 <p class=examplefileCxSpMiddle>wget<span style='mso-tab-count:3'> </span>3DCoffee
11457 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'> </span>Automatic
11458 Downloading of Structures</p>
11460 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11462 <p class=examplefileCxSpMiddle>sap<span style='mso-tab-count:3'> </span>structure/structure
11465 <p class=examplefileCxSpMiddle>(obtain it from W. Taylor, NIMR-MRC).</p>
11467 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11469 <p class=examplefileCxSpMiddle>TMalign<span style='mso-tab-count:2'> </span>zhang.bioinformatics.ku.edu/TM-align/</p>
11471 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11473 <p class=examplefileCxSpMiddle>mustang<span style='mso-tab-count:2'> </span>www.cs.mu.oz.au/~arun/mustang/</p>
11475 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11477 <p class=examplefileCxSpMiddle>wublastclient<span style="mso-spacerun:
11478 yes">
11479 </span>www.ebi.ac.uk/Tools/webservices/clients/wublast</p>
11481 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11483 <p class=examplefileCxSpMiddle>Blast<span style='mso-tab-count:3'> </span><a
11484 href="http://www.ncbi.nih.nlm.gov/">www.ncbi.nih.nlm.gov</a></p>
11486 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11488 <p class=examplefileCxSpMiddle>Fugue*<span style='mso-tab-count:2'> </span>protein
11489 to structure alignment program</p>
11491 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'> </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</p>
11493 <p class=examplefileCxSpLast><span style='mso-tab-count:3'> </span>***NOT
11498 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
11500 <p class=MyNormal><span lang=AF>Once the package is installed, make sure make
11501 sure that the executable is on your path, so that t_coffee can find it
11502 automatically.</span></p>
11504 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
11506 <p class=MyNormal><span lang=AF>The wublast client makes it possible to run
11507 BLAST at the EBI without having to install any database locally. It is an ideal
11508 solution if you are only using expresso occasionally.</span></p>
11510 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
11512 <h3><a name="_Toc151732228">Installing Fugue for T-Coffee</a></h3>
11514 <p class=MyNormal><span lang=AF>Uses a standard fugue installation. You only
11515 need to install the following packages:</span></p>
11517 <p class=MyNormal><span lang=AF><span style="mso-spacerun:
11518 yes"> </span>joy, melody, fugueali, sstruc, hbond</span></p>
11520 <p class=MyNormal><span lang=AF>If you have root privileges, you can install
11521 the common data in: </span></p>
11523 <p class=MyNormal><span lang=AF>cp fugue/classdef.dat<span style='mso-tab-count:
11524 1'> </span>/data/fugue/SUBST/classdef.dat</span></p>
11526 <p class=MyNormal><span lang=AF>otherwise</span></p>
11528 <p class=MyNormal><span lang=AF>Setenv MELODY_CLASSDEF=<location></span></p>
11530 <p class=MyNormal><span lang=AF>Setenv MELODY_SUBST=fugue/allmat.dat</span></p>
11532 <p class=MyNormal><span lang=AF><span style="mso-spacerun: yes"> </span></span></p>
11534 <p class=MyNormal><span lang=AF>All the other configuration files must be in
11535 the right location. </span></p>
11537 <h2><a name="_Toc151732229">Installation of R-Coffee</a></h2>
11539 <p class=MyNormal><span lang=AF>R-Coffee is a special mode able to align RNA
11540 sequences while taking into account their secondary structure.</span><span
11541 style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
11543 <h3><a name="_Toc151732230">Automated Installation</a></h3>
11545 <p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>
11547 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11548 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11549 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11550 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11552 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>./install rcoffee</p>
11556 <p class=MsoNormal><o:p> </o:p></p>
11558 <p class=MyNormal><span lang=AF>In theory, this command should download and
11559 install every required package (except <b>consan</b>). If, however, it fails,
11560 you should switch to the manual installation (see next).</span></p>
11562 <h3><a name="_Toc151732231">Manual Installation</a></h3>
11564 <p class=MyNormal><span lang=AF>R-Coffee only requires the package Vienna to be
11565 installed, in order to compute multiple sequence alignments. To make the best
11566 out of it, you should also have all the packages required by M-Coffee</span></p>
11568 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span></span></p>
11570 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11571 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11572 background:#E6E6E6'>
11574 <p class=examplefileCxSpFirst>Package<span style='mso-tab-count:2'> </span>Function</p>
11576 <p class=examplefileCxSpMiddle>===================================================</p>
11578 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11580 <p class=examplefileCxSpMiddle>consan<span style='mso-tab-count:2'> </span>R-Coffee
11583 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'> </span>Computes
11584 highly accurate pairwise Alignments</p>
11586 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'> </span>***NOT
11589 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'> </span>selab.janelia.org/software/consan/</p>
11591 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11593 <p class=examplefileCxSpMiddle>RNAplfold<span style='mso-tab-count:2'> </span>Computes
11594 RNA secondary Structures </p>
11596 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'> </span>www.tbi.univie.ac.at/~ivo/RNA/</p>
11598 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11600 <p class=examplefileCxSpMiddle>probconsRNA<span style='mso-tab-count:2'> </span>probcons.stanford.edu/</p>
11602 <p class=examplefileCxSpMiddle><span style="mso-spacerun:
11603 yes"> </span></p>
11605 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11607 <p class=examplefileCxSpMiddle>M-Coffee<span style='mso-tab-count:2'> </span>T-Coffee
11608 and the most common MSA Packages</p>
11610 <p class=examplefileCxSpLast><span style='mso-tab-count:3'> </span>(cf
11611 M-Coffee in this installation guide)</p>
11615 <h3><a name="_Toc151732232">Installing ProbbonsRNA for R-Coffee</a></h3>
11617 <p class=MyNormal><span lang=AF>Follow the installation procedure, but make
11618 sure you rename the probcons executable into probconsRNA.</span></p>
11620 <h3><a name="_Toc151732233">Installing Consan for R-Coffee</a></h3>
11622 <p class=MyNormal><span lang=AF>In order to insure a proper interface beween
11623 consan and R-Coffee, you must make sure that the file mix80.mod is in the
11624 directory ~/.t_coffee/mcoffee or in the mcoffee directory otherwise declared.</span></p>
11626 <p class=MsoNormal><o:p> </o:p></p>
11628 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
11629 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
11632 <p class=ChapterTitle><a name="_Toc101065207"></a><a name="_Toc102494676"><span
11633 style='mso-bookmark:_Toc101065207'>Q</span></a>uick Start</p>
11637 <p class=MsoBodyText>We only give you the very basics here. Please use the
11638 Tutorial for more detailed information on how to use our tools.</p>
11640 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
11641 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
11643 <p class=Warning><a name="_Toc101065208"></a><a name="_Toc102494296"></a><a
11644 name="_Toc102494677"><span style='mso-bookmark:_Toc102494296'><span
11645 style='mso-bookmark:_Toc101065208'>IMPORTANT: All the files mentionned here
11646 (sampe_seq...) can be found in the example directory of the distribution.</span></span></a></p>
11650 <h2><span style='mso-bookmark:_Toc102494677'><span style='mso-bookmark:_Toc102494296'><span
11651 style='mso-bookmark:_Toc101065208'><a name="_Toc151732234">T-COFFEE</a></span></span></span></h2>
11653 <p class=MyNormal><span lang=AF>Write your sequences in the same file
11654 (Swiss-prot, Fasta or Pir) and type. </span></p>
11656 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11657 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11658 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11659 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11661 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
11662 sample_seq1.fasta<span style="mso-spacerun: yes"> </span></p>
11666 <p class=MyNormal><span lang=AF>This will output two files:</span></p>
11668 <p class=example2CxSpFirst>sample_seq1.aln: your Multiple Sequence Alignment</p>
11670 <p class=example2CxSpLast>sample_seq1.dnd: The Guide tree (newick Format)</p>
11672 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
11673 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
11675 <p class=Warning>IMPORTANT: </p>
11677 <p class=Warning>In theory nucleic acids should be automatically detected and
11678 the default methods should be adapted appropriately. However, sometimes this
11679 may fail, either because the sequences are too short or contain too many
11680 ambiguity codes. </p>
11682 <p class=Warning>When this happens, you are advised to explicitly set the type
11683 of your sequences</p>
11685 <p class=Warning>NOTE: the –mode=dna is not needed or supported anymore</p>
11689 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11690 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11691 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11692 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11694 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
11695 sample_dnaseq1.fasta –type=dna</p>
11699 <h2><a name="_Toc101065209"></a><a name="_Toc102494297"></a><a
11700 name="_Toc102494678"></a><a name="_Toc151732235"><span style='mso-bookmark:
11701 _Toc102494678'><span style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:
11702 _Toc101065209'>M-Coffee</span></span></span></a><span style='mso-bookmark:_Toc102494678'><span
11703 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'></span></span></span></h2>
11705 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11706 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11707 lang=AF>M-Coffee is a Meta version of T-Coffee that makes it possible to
11708 combine the output of at least eight packages (Muscle, probcons, poa, dialignT,
11709 mafft, clustalw, PCMA and T-Coffee).</span></span></span></span></p>
11711 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11712 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11713 lang=AF>If all these packages are already installed on your machine. You must:</span></span></span></span></p>
11715 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11716 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11717 lang=AF><o:p> </o:p></span></span></span></span></p>
11719 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11720 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11721 lang=AF>1-set the following environment variables</span></span></span></span></p>
11723 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11724 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11725 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11726 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11728 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11729 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11730 style='mso-bookmark:_Toc101065209'><span style='mso-tab-count:1'> </span>export
11731 POA_DIR=[absolute path of the POA installation dir]</span></span></span></p>
11733 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11734 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11735 style='mso-bookmark:_Toc101065209'><span style='mso-tab-count:1'> </span>export
11736 DIALIGNT_DIR=[Absolute path of the DIALIGN-T/conf</span></span></span></p>
11740 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11741 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11742 lang=AF>Once this is done, write your sequences in a file and run: same file
11743 (Swiss-prot, Fasta or Pir) and type. </span></span></span></span></p>
11745 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11746 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11747 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11748 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11750 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11751 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11752 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_seq1.fasta –mode
11753 mcoffee </span></span></span></p>
11757 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11758 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11759 lang=AF>If the program starts complaining one package or the other is missing,
11760 this means you will have to go the hard way and install all these packages
11761 yourself... Proceed to the M-Coffee section for more detailed instructions.</span></span></span></span></p>
11763 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11764 style='mso-bookmark:_Toc101065209'><a name="_Toc151732236">Expresso</a></span></span></span></h2>
11766 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11767 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11768 lang=AF>If you have installed the EBI wublast.pl client, Expresso will BLAST
11769 your sequences against PDB, identify the best targets and use these to align
11770 your proteins.</span></span></span></span></p>
11772 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11773 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11774 lang=AF><o:p> </o:p></span></span></span></span></p>
11776 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11777 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11778 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11779 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11781 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11782 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11783 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_seq1.fasta –mode
11784 expresso</span></span></span></p>
11788 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11789 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11790 lang=AF>If you did not manage to install all the required structural packages
11791 for Expresso, like Fugue or Sap, you can still run expresso by selecting
11792 yourself the structural packages you want to use. For instance, if you'd rather
11793 use TM-Align than sap, try: </span></span></span></span></p>
11795 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11796 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11797 lang=AF><span style='mso-tab-count:1'> </span></span></span></span></span></p>
11799 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11800 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11801 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11802 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11804 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11805 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11806 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_seq1.fasta
11807 –template_file EXPRESSO -method TMalign_pair</span></span></span></p>
11811 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11812 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11813 lang=AF><o:p> </o:p></span></span></span></span></p>
11815 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11816 style='mso-bookmark:_Toc101065209'><a name="_Toc151732237">R-Coffee</a></span></span></span></h2>
11818 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11819 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11820 lang=AF>R-Coffee can be used to align RNA sequences, using their RNApfold
11821 predicted secondary structures. The best results are obtained by using the
11822 consan pairwise method. If you have consan installed:</span></span></span></span></p>
11824 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11825 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11826 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11827 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11829 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11830 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11831 style='mso-bookmark:_Toc101065209'>t_coffee sample_rnaseq1.fasta
11832 –special_mode rcoffee_consan </span></span></span></p>
11836 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11837 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11838 lang=AF>This will only work if your sequences are short enough (less than 200
11839 nucleotides). A good alternative is the rmcoffee mode that will run Muscle,
11840 Probcons4RNA and MAfft and then use the secondary structures predicted by
11841 RNApfold. </span></span></span></span></p>
11843 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11844 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11845 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11846 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11848 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11849 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11850 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_rnaseq1.fasta
11851 –mode mrcoffee </span></span></span></p>
11855 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11856 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11857 lang=AF><o:p> </o:p></span></span></span></span></p>
11859 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11860 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11861 lang=AF>If you want to decide yourself which methods should be combined by
11862 R-Coffee, run:</span></span></span></span></p>
11864 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11865 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11866 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11867 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11869 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11870 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11871 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_rnaseq1.fasta
11872 –mode rcoffee -method lalign_id_pair slow_pair </span></span></span></p>
11876 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11877 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11878 lang=AF><o:p> </o:p></span></span></span></span></p>
11880 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11881 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11882 lang=AF><o:p> </o:p></span></span></span></span></p>
11884 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11885 style='mso-bookmark:_Toc101065209'><br>
11886 <a name="_Toc151732238">iRMSD and APDB</a></span></span></span></h2>
11888 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11889 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11890 lang=AF>All you need is a file containing the alignment of sequences with a
11891 known structure. These sequences must be named according to their PDB ID,
11892 followed by the chain index ( 1aabA for instance). All the sequences do not
11893 need to have a known structure, but at least two need to have it.</span></span></span></span></p>
11895 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11896 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11897 lang=AF>Given the alignment:</span></span></span></span></p>
11899 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11900 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11901 lang=AF><o:p> </o:p></span></span></span></span></p>
11903 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11904 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11905 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11906 background:#FFFFCC;margin-left:42.55pt;margin-right:0cm'>
11908 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11909 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11910 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee –other_pg irmsd -aln
11911 3d_sample4.aln </span></span></span></p>
11915 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11916 style='mso-bookmark:_Toc101065209'><a name="_Toc151732239">tRMSD</a></span></span></span></h2>
11918 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11919 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11920 lang=AF>tRMSD is a structure based clustering method using the iRMSD to drive
11921 the clustering. The T-RMSD supports all the parameters supported by iRMSD or
11922 APDB.</span></span></span></span></p>
11924 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11925 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11926 lang=AF><o:p> </o:p></span></span></span></span></p>
11928 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11929 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11930 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11931 background:#FFFFCC;margin-left:42.55pt;margin-right:0cm'>
11933 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11934 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11935 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee –other_pg trmsd -aln
11936 3d_sample5.aln -template_file 3d_sample5.template_list </span></span></span></p>
11940 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11941 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11942 style='mso-ansi-language:EN-US'>3d_sample5.aln is a multiple alignment in which
11943 each sequence has a known structure. The file </span><span lang=AF>3d_sample5.template_list
11944 is a fasta like file declaring the structure associated with each sequence, in
11945 the form: </span></span></span></span></p>
11947 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11948 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11949 background:#E6E6E6;margin-left:0cm;margin-right:1.0cm'>
11951 <p class=examplefilesmall><span style='mso-bookmark:_Toc102494678'><span
11952 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>>
11953 <seq_name> _P_ <PDB structure file or name> </span></span></span></p>
11957 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11958 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11959 lang=AF><o:p> </o:p></span></span></span></span></p>
11961 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11962 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11963 background:#E6E6E6'>
11965 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494678'><span
11966 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>*******
11967 3d_sample5.template_list ********<span style='mso-tab-count:1'> </span></span></span></span></p>
11969 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11970 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>>2UWI-3A
11971 _P_ 2UWI-3.pdb</span></span></span></p>
11973 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11974 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>>2UWI-2A
11975 _P_ 2UWI-2.pdb</span></span></span></p>
11977 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11978 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>>2UWI-1A
11979 _P_ 2UWI-1.pdb</span></span></span></p>
11981 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11982 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>>2HEY-4R
11983 _P_ 2HEY-4.pdb</span></span></span></p>
11985 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11986 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>...</span></span></span></p>
11988 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494678'><span
11989 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>**************************************</span></span></span></p>
11993 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11994 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11995 lang=AF><o:p> </o:p></span></span></span></span></p>
11997 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11998 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11999 lang=AF>The program then outputs a series of files</span></span></span></span></p>
12001 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
12002 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
12003 background:#E6E6E6'>
12005 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494678'><span
12006 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12007 style='font-size:8.0pt'>Template Type: [3d_sample5.template_list] Mode Or File:
12008 [3d_sample5.template_list] [Start]<o:p></o:p></span></span></span></span></p>
12010 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12011 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12012 style='font-size:8.0pt'><span style="mso-spacerun:
12013 yes"> </span>[Sample
12014 Columns][TOT=<span style="mso-spacerun: yes"> </span>51][100
12015 %][ELAPSED TIME:<span style="mso-spacerun: yes"> </span>0
12016 sec.]<o:p></o:p></span></span></span></span></p>
12018 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12019 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12020 style='font-size:8.0pt'><span style="mso-spacerun:
12021 yes"> </span>[Tree
12022 Cmp][TOT=<span style="mso-spacerun: yes"> </span>13][ 92 %][ELAPSED
12023 TIME:<span style="mso-spacerun: yes"> </span>0 sec.]<o:p></o:p></span></span></span></span></p>
12025 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12026 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12027 style='font-size:8.0pt'><span style="mso-spacerun: yes"> </span>#### File
12028 Type=<span style="mso-spacerun: yes"> </span>TreeList Format=<span
12029 style="mso-spacerun: yes"> </span>newick Name=
12030 3d_sample5.tot_pos_list<o:p></o:p></span></span></span></span></p>
12032 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12033 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12034 style='font-size:8.0pt'><span style="mso-spacerun: yes"> </span>#### File
12035 Type=<span style="mso-spacerun: yes">
12036 </span>Tree Format=<span style="mso-spacerun: yes">
12037 </span>newick Name= 3d_sample5.struc_tree10<o:p></o:p></span></span></span></span></p>
12039 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12040 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12041 style='font-size:8.0pt'><span style="mso-spacerun: yes"> </span>#### File
12042 Type=<span style="mso-spacerun: yes">
12043 </span>Tree Format=<span style="mso-spacerun: yes">
12044 </span>newick Name= 3d_sample5.struc_tree50<o:p></o:p></span></span></span></span></p>
12046 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12047 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12048 style='font-size:8.0pt'><span style="mso-spacerun: yes"> </span>#### File
12049 Type=<span style="mso-spacerun: yes">
12050 </span>Tree Format=<span style="mso-spacerun: yes">
12051 </span>newick Name= 3d_sample5.struc_tree100<o:p></o:p></span></span></span></span></p>
12053 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12054 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12055 style='font-size:8.0pt'><span style="mso-spacerun: yes"> </span>#### File
12056 Type= Colored MSA Format= score_html Name= 3d_sample5.struc_tree.html<o:p></o:p></span></span></span></span></p>
12058 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494678'><span
12059 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><o:p> </o:p></span></span></span></p>
12063 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12064 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12065 lang=AF><o:p> </o:p></span></span></span></span></p>
12067 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12068 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12069 lang=AF>3d_sample5.tot_pos_list <span style='mso-tab-count:1'> </span>is
12070 a list of the tRMSD tree associated with every position. </span></span></span></span></p>
12072 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12073 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12074 lang=AF>3d_sample5.struc_tree100<span style='mso-tab-count:1'> </span>is
12075 a consensus tree (phylip/consense) of the trees contained in the previous file.
12076 <b>This file is the default output<o:p></o:p></b></span></span></span></span></p>
12078 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12079 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12080 lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'> </span>is
12081 a consensus tree (phylip/consense) of the 10% trees having the higest average
12082 agreement with the rest</span></span></span></span></p>
12084 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12085 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12086 lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'> </span>is
12087 a consensus tree (phylip/consense) of the 50% trees having the higest average
12088 agreement with the rest</span></span></span></span></p>
12090 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12091 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12092 lang=AF>3d_sample5.html<span style='mso-tab-count:1'> </span>is
12093 a colored version of the output showing in red the positions that give the
12094 highest support to 3d_sample5.struc_tree100</span></span></span></span></p>
12096 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12097 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12098 lang=AF><o:p> </o:p></span></span></span></span></p>
12100 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12101 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12102 lang=AF><o:p> </o:p></span></span></span></span></p>
12104 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12105 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12106 lang=AF><o:p> </o:p></span></span></span></span></p>
12108 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
12109 style='mso-bookmark:_Toc101065209'><a name="_Toc151732240">MOCCA</a></span></span></span></h2>
12111 <p class=MyNormal><span lang=AF>Write your sequences in the same file
12112 (Swiss-prot, Fasta or Pir) and type. </span></p>
12114 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12115 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12116 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12117 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12119 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12120 –other_pg mocca sample_seq1.fasta </p>
12124 <p class=MyNormal><span lang=AF>This command output one files (<your
12125 sequences>.mocca_lib) and starts an interactive menu. </span></p>
12127 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
12128 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
12131 <p class=ChapterTitle><a name="_Toc101065210"></a><a name="_Toc102494679"><span
12132 style='mso-bookmark:_Toc101065210'>Recent M</span></a>odifications</p>
12136 <p class=MyNormal><span lang=AF>Warning: This log of recent modifications is
12137 not as thorough and accurate as it should be.</span></p>
12139 <p class=MyNormal><span lang=AF>-9.86 New data structure for the primary
12140 library that results in highly improved running times for mcoffee and
12141 significantly decreased memory usage.</span></p>
12143 <p class=MyNormal><span lang=AF>-5.80 Novel assembly algorithm
12144 (linked_pair_wise) and the primary library is now made of probcons style
12145 pairwise alignments (proba_pair)</span></p>
12147 <p class=MyNormal><span lang=AF>-4.30 and upward: the FAQ has moved into a new
12148 tutorial document</span></p>
12150 <p class=MyNormal><span lang=AF>-4.30 and upward: -in has will be deprecated
12151 and replaced by the flags: -profile,-method,-aln,-seq,-pdb</span></p>
12153 <p class=MyNormal><span lang=AF>-4.02: -mode=dna is still available but not any
12154 more needed or supported. Use type=protein or dna if you need to force things</span></p>
12156 <p class=MyNormal><b style='mso-bidi-font-weight:normal'><span lang=AF>-</span></b><span
12157 lang=AF>3.28: corrected a bug that prevents short sequences from being
12158 correctly aligned</span></p>
12160 <p class=MyNormal><span lang=AF>-Use of @ as a separator when specifying
12161 methods parameters</span></p>
12163 <p class=MyNormal><span lang=AF>-The most notable modifications have to do with
12164 the structure of the input. From version 2.20, all files must be tagged to
12165 indicate their nature (A: alignment, S: Sequence, L: Library
\85). We are becoming
12166 stricter, but that
\92s for your own good
\85 </span></p>
12168 <p class=MyNormal><span lang=AF>Another important modification has to do with
12169 the flag -matrix: it now controls the matrix being used for the computation </span></p>
12171 <span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:
12172 "Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;
12173 mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:always'>
12176 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
12177 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
12180 <p class=ChapterTitle>Reference Manual</p>
12184 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
12186 <p class=MyNormal><span lang=AF>This reference manual gives a list of all the
12187 flags that can be used to modify the behavior of T-Coffee. For your
12188 convenience, we have grouped them according to their nature. To display a list
12189 of all the flags used in the version of T-Coffee you are using (along with
12190 their default value), type:</span></p>
12192 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12193 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12194 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12195 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12197 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee </p>
12201 <p class=MyNormal><span lang=AF>Or</span></p>
12203 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12204 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12205 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12206 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12208 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12213 <p class=MyNormal><span lang=AF>Or</span></p>
12215 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12216 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12217 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12218 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12220 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12221 –help –in<span class=MyNormalChar><span style='font-size:11.0pt;
12222 mso-ansi-language:EN-US'><o:p></o:p></span></span></p>
12226 <p class=MyNormal><span lang=AF>Or any other parameter</span></p>
12228 <h2><a name="_Toc101065212"></a><a name="_Toc102494358"></a><a
12229 name="_Toc102494743"><span style='mso-bookmark:_Toc102494358'><span
12230 style='mso-bookmark:_Toc101065212'><o:p> </o:p></span></span></a></h2>
12232 <h2><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12233 style='mso-bookmark:_Toc101065212'><a name="_Toc151732241">Environment
12234 Variables</a></span></span></span></h2>
12236 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12237 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>It
12238 is possible to modify T-Coffee
\92s behavior by setting any of the following
12239 environment variables. On the bash shell, use export VAR=
\94value
\94. On the
12240 cshell, use set $VAR=
\94xxx
\94</span></span></span></p>
12242 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12243 style='mso-bookmark:_Toc101065212'><o:p> </o:p></span></span></span></h3>
12245 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12246 style='mso-bookmark:_Toc101065212'><a name="_Toc151732242">http_proxy_4_TCOFFEE</a></span></span></span></h3>
12248 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12249 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12250 lang=AF>Sets the http_proxy and HTTP_proxy values used by T-Coffee. </span></span></span></span></p>
12252 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12253 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12254 lang=AF>These values get supersede http_proxy and HTTP_proxy.
12255 http_proxy_4_TCOFFEE gets superseded by the command line values (-proxy and
12256 -email)</span></span></span></span></p>
12258 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12259 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12260 lang=AF>If you have no proxy, just set this value to an empty string.</span></span></span></span></p>
12262 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12263 style='mso-bookmark:_Toc101065212'><a name="_Toc151732243">email_4_TCOFFEE</a></span></span></span></h3>
12265 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12266 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12267 lang=AF>Set the E-mail values provided to web services called upon by T-Coffee.
12268 Can be over-riden by the flag <i>-email.<o:p></o:p></i></span></span></span></span></p>
12270 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12271 style='mso-bookmark:_Toc101065212'><a name="_Toc151732244">DIR_4_TCOFFEE</a></span></span></span></h3>
12273 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12274 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12275 lang=AF>By default this variable is set to $HOME/.t_coffee. This is where
12276 T-Coffee expects to find its cache, tmp dir and possibly any temporary data
12277 stored by the program.</span></span></span></span></p>
12279 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12280 style='mso-bookmark:_Toc101065212'><a name="_Toc151732245">TMP_4_TCOFFEE</a></span></span></span></h3>
12282 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12283 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12284 lang=AF>By default this variable is set to $HOME/.t_coffee/tmp. This is where
12285 T-Coffee stores temporary files.</span></span></span></span></p>
12287 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12288 style='mso-bookmark:_Toc101065212'><a name="_Toc151732246">CACHE_4_TCOFFEE</a></span></span></span></h3>
12290 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12291 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12292 lang=AF>By default this variable is set to $HOME/.t_coffee/cache. This is where
12293 T-Coffee stores any data expensive to obtain: pdb files, sap alignments....</span></span></span></span></p>
12295 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12296 style='mso-bookmark:_Toc101065212'><a name="_Toc151732247">PLUGINS_4_TCOFFEE</a></span></span></span></h3>
12298 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12299 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12300 lang=AF>By default all the companion packages are searched in the directory
12301 DIR_4_TCOFFEE/plugins/<OS>. This variable overrides the default. This
12302 variable can also be overriden by the <i>-plugins</i> T-Coffee flag</span></span></span></span></p>
12304 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12305 style='mso-bookmark:_Toc101065212'><a name="_Toc151732248">NO_ERROR_REPORT_4_TCOFFEE</a></span></span></span></h3>
12307 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12308 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12309 lang=AF>By default this variable is no set. Set it if you do not want the
12310 program to generate a verbose error output file (useful for running a server).</span></span></span></span></p>
12312 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12313 style='mso-bookmark:_Toc101065212'><a name="_Toc151732249">PDB_DIR</a></span></span></span></h3>
12315 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12316 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12317 lang=AF>Indicate the location of your local PDB installation.</span></span></span></span></p>
12319 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12320 style='mso-bookmark:_Toc101065212'><a name="_Toc151732250">NO_WARNING_4_TCOFFEE</a></span></span></span></h3>
12322 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12323 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12324 lang=AF>Suppresses all the warnings.</span></span></span></span></p>
12326 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12327 style='mso-bookmark:_Toc101065212'><a name="_Toc151732251">UNIQUE_DIR_4_TCOFFEE</a></span></span></span></h3>
12329 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12330 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12331 lang=AF>Sets:</span></span></span></span></p>
12333 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12334 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12335 lang=AF><span style='mso-tab-count:1'> </span>DIR_4_TCOFFEE</span></span></span></span></p>
12337 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12338 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12339 lang=AF><span style='mso-tab-count:1'> </span>CACHE_4_TCOFFEE</span></span></span></span></p>
12341 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12342 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12343 lang=AF><span style='mso-tab-count:1'> </span>TMP_4_TCOFFEE</span></span></span></span></p>
12345 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12346 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12347 lang=AF><span style='mso-tab-count:1'> </span>PLUGINS_4_TCOFFEE</span></span></span></span></p>
12349 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12350 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12351 lang=AF>To the same unique value. The string MUST be a valid directory<span
12352 style='mso-tab-count:1'> </span></span></span></span></span></p>
12354 <h2><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12355 style='mso-bookmark:_Toc101065212'><a name="_Toc151732252">Setting up the
12356 T-Coffee environment variables</a></span></span></span></h2>
12358 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12359 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>T-Coffee
12360 can have its own environment file. This environment is kept in a file named
12361 $HOME/.t_coffee/t_coffee_env and can be edited. The value of any legal variable
12362 can be modified through that file. For instance, here is an example of a
12363 configuration file when not requiring a proxy.</span></span></span></p>
12365 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
12366 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
12367 background:#E6E6E6'>
12369 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494743'><span
12370 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>http_proxy_4_TCOFFEE=</span></span></span></p>
12372 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494743'><span
12373 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>EMAIL_4_TCOFFEE=cedric.notredame@europe.com</span></span></span></p>
12377 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12378 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>If
12379 you want to use a specific configuration file:</span></span></span></p>
12381 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12382 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12383 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12384 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12386 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
12387 style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12388 style='mso-bookmark:_Toc101065212'>t_coffee
\85 -setenv
12389 ENV_4_TCOFFEE=<location></span></span></span></p>
12393 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12394 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>In
12395 general, you can set any environment variable using the –setenv flag. You
12396 can also simply do an export:</span></span></span></p>
12398 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12399 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12400 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12401 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12403 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
12404 style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12405 style='mso-bookmark:_Toc101065212'>export ENV_4_TCOFFEE=<location></span></span></span></p>
12409 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
12410 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
12412 <p class=Warning><span style='mso-bookmark:_Toc102494743'><span
12413 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>IMPORTANT:
12414 </span></span></span></p>
12416 <p class=Warning style='text-align:justify;text-indent:35.4pt;background:#F7CBB7'><span
12417 style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12418 style='mso-bookmark:_Toc101065212'>export > –setenv > -proxy,
12419 -email > t_coffee_env > default<span style="mso-spacerun: yes">
12420 </span>environment</span></span></span></p>
12422 <p class=Warning style='text-align:justify;background:#F7CBB7'><span
12423 style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12424 style='mso-bookmark:_Toc101065212'><o:p> </o:p></span></span></span></p>
12428 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12429 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>Note
12430 that when you use –setenv for <b style='mso-bidi-font-weight:normal'>PATH,</b>
12431 the value you provide is concatenated <b style='mso-bidi-font-weight:normal'>TO
12432 THE BEGINNING </b>of the current PATH value. This way you can force T-Coffee to
12433 use a specific version of an aligner.</span></span></span></p>
12435 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12436 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><o:p> </o:p></span></span></span></p>
12438 <h2><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12439 style='mso-bookmark:_Toc101065212'><a name="_Toc151732253">Well Behaved
12440 Parameters</a></span></span></span></h2>
12442 <h3><a name="_Toc101065213"></a><a name="_Toc102494359"></a><a
12443 name="_Toc102494744"></a><a name="_Toc151732254"><span style='mso-bookmark:
12444 _Toc102494744'><span style='mso-bookmark:_Toc102494359'><span style='mso-bookmark:
12445 _Toc101065213'>Separation</span></span></span></a></h3>
12447 <p class=MyNormal><span lang=AF>You can use any kind of separator you want
12448 (i.e. ,; <space>=). The syntax used in this document is meant to be
12449 consistent with that of ClustalW. However, in order to take advantage of the
12450 automatic filename compleation provided by many shells, you can replace
\93=
\94 and
12451 \93,
\94 with a space.</span></p>
12453 <h3><a name="_Toc101065214"></a><a name="_Toc102494360"></a><a
12454 name="_Toc102494745"></a><a name="_Toc151732255"><span style='mso-bookmark:
12455 _Toc102494745'><span style='mso-bookmark:_Toc102494360'><span style='mso-bookmark:
12456 _Toc101065214'>Posix</span></span></span></a></h3>
12458 <p class=MyNormal><span lang=AF>T-Coffee is not POSIX compliant (sorry </span><span
12459 lang=AF style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
12460 mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
12461 Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>L</span></span><span
12462 lang=AF>).</span></p>
12464 <h3><a name="_Toc101065215"></a><a name="_Toc102494361"></a><a
12465 name="_Toc102494746"></a><a name="_Toc151732256"><span style='mso-bookmark:
12466 _Toc102494746'><span style='mso-bookmark:_Toc102494361'><span style='mso-bookmark:
12467 _Toc101065215'>Entering the right parameters</span></span></span></a></h3>
12469 <p class=MyNormal><span lang=AF>There are many ways to enter parameters in T-Coffee,
12470 see the -parameter flag in </span></p>
12472 <p class=Noteboxtitle><o:p> </o:p></p>
12474 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
12475 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
12477 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
12478 style='text-align:center;background:#FFFF89'><span style='font-size:20.0pt;
12479 mso-bidi-font-size:10.0pt'>Parameters Priority<o:p></o:p></span></p>
12481 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p> </o:p></p>
12483 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>In general you will
12484 not need to use these complicated parameters. Yet, if you find yourself typing
12485 long command lines on a regular basis, it may be worth reading this section.</p>
12487 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p> </o:p></p>
12489 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>One may easily feel
12490 confused with the various manners in which the parameters can be passed to
12491 t_coffee. The reason for these many mechanisms is that they allow several
12492 levels of intervention. For instance, you may install t_coffee for all the
12493 users and decide that the defaults we provide are not the proper ones
\85 In this
12494 case, you will need to make your own t_coffee_default file.</p>
12496 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p> </o:p></p>
12498 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>Later on, a user
12499 may find that he/she needs to keep re-using a specific set of parameters,
12500 different from those in t_coffee_default, hence the possibility to write an
12501 extra parameter file: parameters. In summary:</p>
12503 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p> </o:p></p>
12505 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>-parameters >
12506 prompt parameters > -t_coffee_defaults > -mode</p>
12508 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p> </o:p></p>
12510 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>This means that -<i>parameters</i>
12511 supersede all the others, while parameters provided via -<i>special mode</i>
12512 are the weakest.</p>
12516 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
12518 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
12520 <h2><a name="_Toc101065216"></a><a name="_Toc102494362"></a><a
12521 name="_Toc102494747"></a><a name="_Toc151732257"><span style='mso-bookmark:
12522 _Toc102494747'><span style='mso-bookmark:_Toc102494362'><span style='mso-bookmark:
12523 _Toc101065216'>Parameters Syntax</span></span></span></a></h2>
12525 <p class=flag><a name="_Toc101065218"></a><a name="_Toc102494748"></a><a
12526 name="_Toc151732258"><span style='mso-bookmark:_Toc102494748'><span
12527 style='mso-bookmark:_Toc101065218'><span lang=AF>No Flag</span></span></span></a></p>
12529 <p class=flagdescription>If no flag is used<b style='mso-bidi-font-weight:normal'>
12530 </b><i style='mso-bidi-font-style:normal'><your sequence> </i>must be the
12531 first argument. See format for further information.</p>
12533 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12534 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12535 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12536 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12538 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12539 sample_seq1.fasta </p>
12543 <p class=flagdescription>Which is equivalent to</p>
12545 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12546 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12547 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12548 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12550 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12551 Ssample_seq1.fasta </p>
12555 <p class=flagdescription>When you do so, <b style='mso-bidi-font-weight:normal'>sample_seq1</b>
12556 is used as a name prefix for every file the program outputs.</p>
12558 <p class=flag><a name="_Toc101065219"></a><a name="_Toc102494749"></a><a
12559 name="_Toc151732259"><span style='mso-bookmark:_Toc102494749'><span
12560 style='mso-bookmark:_Toc101065219'><span lang=AF>-parameters</span></span></span></a><span
12561 lang=AF style='background:gray;mso-highlight:gray'><o:p></o:p></span></p>
12563 <p class=flagusage><span lang=FR>Usage: -parameters=parameters_file</span></p>
12565 <p class=instruction>Default: no parameters file</p>
12567 <p class=flagdescription>Indicates a file containing extra parameters.
12568 Parameters read this way behave as if they had been added on the right end of
12569 the command line that they either supersede(one value parameter) or complete
12570 (list of values). For instance, the following file (parameter.file) could be
12573 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
12574 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
12575 background:#E6E6E6'>
12577 <p class=examplefileCxSpFirst>*******sample_param_file.param********<span
12578 style='mso-tab-count:1'> </span></p>
12580 <p class=examplefileCxSpMiddle><span style='mso-tab-count:1'> </span>-in=Ssample_seq1.fasta,Mfast_pair</p>
12582 <p class=examplefileCxSpMiddle><span style='mso-tab-count:1'> </span>-output=msf_aln</p>
12584 <p class=examplefileCxSpLast>**************************************</p>
12588 <p class=Note><span style='mso-ansi-language:EN-US'>Note: This is one of the
12589 exceptions (with –infile) where the identifier tag (S,A,L,M
\85) can be
12590 omitted. Any dataset provided this way will be assumed to be a sequence (S).
12591 These exceptions have been designed to keep the program compatible with
12592 ClustalW.<o:p></o:p></span></p>
12594 <p class=Note><span style='mso-ansi-language:EN-US'>Note: This parameter file
12595 can ONLY contain valid parameters. Comments are not allowed. Parameters passed
12596 this way will be checked like normal parameters.<o:p></o:p></span></p>
12598 <p class=flagdescription>Used with:</p>
12600 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12601 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12602 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12603 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12605 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12606 -parameters=sample_param_file.param</p>
12610 <p class=flagdescription>Will cause t_coffee to apply the fast_pair method onto
12611 to the sequences contained in sample_seq.fasta. If you wish, you can also pipe
12612 these arguments into t_coffee, by naming the parameter file "stdin"
12613 (as a rule, any file named stdin is expected to receive its content via the
12616 <p class=example2>cat sample_param_file.param<span style="mso-spacerun:
12617 yes"> </span>| t_coffee -parameters=stdin <a name="_Toc101065220"></a></p>
12619 <p class=flag><span style='mso-bookmark:_Toc101065220'><a name="_Toc102494750"></a><a
12620 name="_Toc151732260"><span style='mso-bookmark:_Toc102494750'><span lang=AF>-t_coffee_defaults</span></span></a></span></p>
12622 <p class=flagusage><span lang=FR>Usage: -t_coffee_defaults=<file_name></span></p>
12624 <p class=instruction>Default: not used.</p>
12626 <p class=flagdescription>This flag tells the program to use some default
12627 parameter file for t_coffee. The format of that file is the same as the one
12628 used with -parameters. The file used is either:</p>
12630 <p class=flagdescription><span style='mso-tab-count:1'> </span>1.
12631 <file name> if a name has been specified</p>
12633 <p class=flagdescription><span style='mso-tab-count:1'> </span>2.<span
12634 style="mso-spacerun: yes"> </span><b>~/.t_coffee_defaults </b>if no file
12637 <p class=flagdescription><span style='mso-tab-count:1'> </span>3.
12638 The file indicated by the environment variable <b>TCOFFEE_DEFAULTS</b></p>
12640 <p class=flag><a name="_Toc151732261"><span lang=AF>-mode</span></a></p>
12642 <p class=flagusage><span lang=FR>Usage: -mode= hard coded mode</span></p>
12644 <p class=instruction>Default: not used.</p>
12646 <p class=flagdescription>It indicates that t_coffee will use some hard coded
12647 parameters. These include:</p>
12649 <p class=flagdescription><span style='mso-tab-count:1'> </span><b
12650 style='mso-bidi-font-weight:normal'>quickaln</b>: very fast approximate
12653 <p class=flagdescription><span style='mso-tab-count:1'> </span><b
12654 style='mso-bidi-font-weight:normal'>dali</b>: a mode used to combine dali
12655 pairwise alignments</p>
12657 <p class=flagdescription><span style='mso-tab-count:1'> </span><b
12658 style='mso-bidi-font-weight:normal'>evaluate</b>: defaults for evaluating an
12661 <p class=flagdescription><span style='mso-tab-count:1'> </span><b
12662 style='mso-bidi-font-weight:normal'>3dcoffee</b>: runs t_coffee with the
12663 3dcoffee parameterization</p>
12665 <p class=flagdescription><o:p> </o:p></p>
12667 <p class=flagdescription>Other modes exist that are not yet fully supported<span
12668 style='mso-tab-count:1'> </span></p>
12670 <p class=flag><a name="_Toc101065222"></a><a name="_Toc102494752"></a><a
12671 name="_Toc151732262"><span style='mso-bookmark:_Toc102494752'><span
12672 style='mso-bookmark:_Toc101065222'><span lang=AF>-score</span></span><span
12673 lang=AF> [Deprecated]</span></span></a></p>
12675 <p class=flagusage><span lang=FR>Usage: -score</span></p>
12677 <p class=instruction>Default: not used</p>
12679 <p class=flagdescription>Toggles on the evaluate mode and causes t_coffee to
12680 evaluates a precomputed alignment provided via <b>-infile=<alignment></b>.
12681 The flag <b>-output</b> must be set to an appropriate format (i.e.
12682 -output=score_ascii, score_html or score_pdf). A better default
12683 parameterization is obtained when using the flag <b>-mode=evaluate.</b></p>
12685 <p class=flag><a name="_Toc102494753"></a><a name="_Toc151732263"><span
12686 style='mso-bookmark:_Toc102494753'><span lang=AF>-evaluate</span></span></a></p>
12688 <p class=flagusage><span lang=FR>Usage: -evaluate</span></p>
12690 <p class=instruction>Default: not used</p>
12692 <p class=flagdescription>Replaces –score. This flag toggles on the
12693 evaluate mode and causes t_coffee to evaluates a pre-computed alignment
12694 provided via <b>-infile=<alignment></b>. The flag <b>-output</b> must be
12695 set to an appropriate format (i.e. -output=score_ascii, score_html or
12698 <p class=flagdescription><o:p> </o:p></p>
12700 <p class=flagdescription>The main purpose of –evaluate is to let you
12701 control every aspect of the evaluation. Yet it is advisable to use pre-defined
12702 parameterization: <b>mode=evaluate.</b></p>
12704 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12705 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12706 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12707 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12709 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12710 –infile=sample_aln1.aln -mode=evaluate </p>
12712 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12713 –infile=sample_seq1.aln –in<span style="mso-spacerun: yes">
12714 </span>Lsample_lib1.tc_lib –mode=evaluate </p>
12718 <p class=flag><a name="_Toc101065223"></a><a name="_Toc102494754"></a><a
12719 name="_Toc151732264"><span style='mso-bookmark:_Toc102494754'><span
12720 style='mso-bookmark:_Toc101065223'><span lang=AF>-convert [cw]</span></span></span></a></p>
12722 <p class=flagusage><span lang=FR>Usage: -convert</span></p>
12724 <p class=instruction>Default: turned off</p>
12726 <p class=flagdescription>Toggles on the conversion mode and causes T-Coffee to
12727 convert the sequences, alignments, libraries or structures provided via the <b>-infile</b>
12728 and <b>-in</b> flags. The output format must be set via the <b>-output</b>
12729 flag. This flag can also be used if you simply want to compute a library (i.e.
12730 you have an alignment and you want to turn it into a library).</p>
12732 <p class=flagdescription>This flag is ClustalW compliant.</p>
12734 <p class=flag><a name="_Toc101065224"></a><a name="_Toc102494755"></a><a
12735 name="_Toc151732265"><span style='mso-bookmark:_Toc102494755'><span
12736 style='mso-bookmark:_Toc101065224'><span lang=AF>-do_align [cw]</span></span></span></a></p>
12738 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
12739 </span>-do_align</span></p>
12741 <p class=instruction>Default: turned on</p>
12743 <h2><a name="_Toc101065225"></a><a name="_Toc102494363"></a><a
12744 name="_Toc102494756"></a><a name="_Toc151732266"><span style='mso-bookmark:
12745 _Toc102494756'><span style='mso-bookmark:_Toc102494363'><span style='mso-bookmark:
12746 _Toc101065225'>Special Parameters</span></span></span></a></h2>
12748 <p class=flag><a name="_Toc101065226"></a><a name="_Toc102494757"></a><a
12749 name="_Toc151732267"><span style='mso-bookmark:_Toc102494757'><span
12750 style='mso-bookmark:_Toc101065226'><span lang=AF>-version</span></span></span></a></p>
12752 <p class=flagusage><span lang=FR>Usage: -version</span></p>
12754 <p class=instruction>Default: not used</p>
12756 <p class=flagdescription>Returns the current version number</p>
12758 <p class=flag><a name="_Toc101065227"></a><a name="_Toc102494758"></a><a
12759 name="_Toc151732268"><span style='mso-bookmark:_Toc102494758'><span
12760 style='mso-bookmark:_Toc101065227'><span lang=AF>-proxy</span></span></span></a><span
12761 style='mso-bookmark:_Toc102494758'><span style='mso-bookmark:_Toc101065227'></span></span></p>
12763 <p class=flagusage><span style='mso-bookmark:_Toc102494758'><span
12764 style='mso-bookmark:_Toc101065227'><span lang=FR>Usage: -proxy=<proxy></span></span></span></p>
12766 <p class=instruction><span style='mso-bookmark:_Toc102494758'><span
12767 style='mso-bookmark:_Toc101065227'>Default: not used</span></span></p>
12769 <p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
12770 style='mso-bookmark:_Toc101065227'>Sets the proxy used by HTTP_proxy AND
12771 http_proxy. Setting with the propmpt supersedes ANY other setting.</span></span></p>
12773 <p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
12774 style='mso-bookmark:_Toc101065227'>Note that if you use no proxy, you should
12775 set</span></span></p>
12777 <p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
12778 style='mso-bookmark:_Toc101065227'><span style='mso-tab-count:1'> </span>-proxy</span></span></p>
12780 <p class=flag><span style='mso-bookmark:_Toc102494758'><span style='mso-bookmark:
12781 _Toc101065227'><a name="_Toc151732269"><span lang=AF>-email</span></a></span></span></p>
12783 <p class=flagusage><span style='mso-bookmark:_Toc102494758'><span
12784 style='mso-bookmark:_Toc101065227'><span lang=FR>Usage: -email=<email></span></span></span></p>
12786 <p class=instruction><span style='mso-bookmark:_Toc102494758'><span
12787 style='mso-bookmark:_Toc101065227'>Default: not used</span></span></p>
12789 <p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
12790 style='mso-bookmark:_Toc101065227'>Sets your email value as provided to web
12791 services</span></span></p>
12793 <p class=flag><span style='mso-bookmark:_Toc102494758'><span style='mso-bookmark:
12794 _Toc101065227'><a name="_Toc151732270"><span lang=AF>-check_configuration</span></a></span></span></p>
12796 <p class=flagusage><span lang=FR>Usage: -check_configuration</span></p>
12798 <p class=instruction>Default: not used</p>
12800 <p class=flagdescription>Checks your system to determine whether all the
12801 programs T-Coffee can interact with are installed.</p>
12803 <p class=flag><a name="_Toc101065228"></a><a name="_Toc102494759"></a><a
12804 name="_Toc151732271"><span style='mso-bookmark:_Toc102494759'><span
12805 style='mso-bookmark:_Toc101065228'><span lang=AF>-cache</span></span></span></a></p>
12807 <p class=flagusage><span lang=FR>Usage: -cache=<use, update, ignore,
12808 <filename>></span></p>
12810 <p class=instruction>Default: -cache=use</p>
12812 <p class=flagdescription>By default, t_coffee stores in a cache directory, the
12813 results of computationally expensive (structural alignment) or network
12814 intensive (BLAST search) operations.<a name="_Toc101065229"></a></p>
12816 <p class=flag><span style='mso-bookmark:_Toc101065229'><a name="_Toc102494760"></a><a
12817 name="_Toc151732272"><span style='mso-bookmark:_Toc102494760'><span lang=AF>-update</span></span></a></span></p>
12819 <p class=flagusage><span lang=FR>Usage: -update</span></p>
12821 <p class=instruction>Default: turned off</p>
12823 <p class=flagdescription>Causes a <span
12824 class=StyleflagdescriptionBoldItalicChar>wget</span> access that checks whether
12825 the t_coffee version you are using needs updating.<a name="_Toc101065230"></a></p>
12827 <p class=flag><span style='mso-bookmark:_Toc101065230'><a name="_Toc102494761"></a><a
12828 name="_Toc151732273"><span style='mso-bookmark:_Toc102494761'><span lang=AF>-full_log</span></span></a></span></p>
12830 <p class=flagusage><span lang=FR>Usage: -full_log=<filename></span></p>
12832 <p class=instruction>Default: turned off</p>
12834 <p class=flagdescription>Causes t_coffee to output a full log file that
12835 contains all the input/output files.<a name="_Toc101065231"></a></p>
12837 <p class=flag><span style='mso-bookmark:_Toc101065231'><a name="_Toc102494762"></a><a
12838 name="_Toc151732274"><span style='mso-bookmark:_Toc102494762'><span lang=AF>-plugins</span></span></a><span
12839 style='mso-bookmark:_Toc102494762'></span></span></p>
12841 <p class=flagusage><span style='mso-bookmark:_Toc101065231'><span
12842 style='mso-bookmark:_Toc102494762'><span lang=FR>Usage: -plugins=<dir></span></span></span></p>
12844 <p class=instruction><span style='mso-bookmark:_Toc101065231'><span
12845 style='mso-bookmark:_Toc102494762'>Default: default</span></span></p>
12847 <p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span
12848 style='mso-bookmark:_Toc102494762'>Specifies the directory in which the
12849 companion packages (other multiple aligners used by M-Coffee, structural
12850 aligners, etc
\85) are kept as an alternative, you can also set the environment
12851 variable PLUGINS_4_TCOFFEE</span></span></p>
12853 <p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span
12854 style='mso-bookmark:_Toc102494762'>The default is ~/.t_coffee/plugins/</span></span></p>
12856 <p class=flag><span style='mso-bookmark:_Toc101065231'><span style='mso-bookmark:
12857 _Toc102494762'><a name="_Toc151732275"><span lang=AF>-other_pg</span></a></span></span></p>
12859 <p class=flagusage><span lang=FR>Usage: -other_pg=<filename></span></p>
12861 <p class=instruction>Default: turned off</p>
12863 <p class=flagdescription>Some rumours claim that Tetris is embedded within
12864 T-Coffee and could be ran using some special set of commands. We wish to deny
12865 these rumours, although we may admit that several interesting reformatting
12866 programs are now embedded in t_coffee and can be ran through the
12867 –other_pg flag.</p>
12869 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12870 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12871 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12872 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12874 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12875 –other_pg=seq_reformat </p>
12877 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12878 –other_pg=unpack_all </p>
12880 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12881 –other_pg=unpack_extract_from_pdb </p>
12885 <h2><a name="_Toc101065232"></a><a name="_Toc102494364"></a><a
12886 name="_Toc102494763"></a><a name="_Toc151732276"><span style='mso-bookmark:
12887 _Toc102494763'><span style='mso-bookmark:_Toc102494364'><span style='mso-bookmark:
12888 _Toc101065232'>Input</span></span></span></a> </h2>
12890 <h3><a name="_Toc101065233"></a><a name="_Toc102494365"></a><a
12891 name="_Toc102494764"></a><a name="_Toc151732277"><span style='mso-bookmark:
12892 _Toc102494764'><span style='mso-bookmark:_Toc102494365'><span style='mso-bookmark:
12893 _Toc101065233'>Sequence Input</span></span></span></a></h3>
12895 <p class=flag><a name="_Toc101065234"></a><a name="_Toc102494765"></a><a
12896 name="_Toc151732278"><span style='mso-bookmark:_Toc102494765'><span
12897 style='mso-bookmark:_Toc101065234'><span lang=AF>-infile [cw]</span></span></span></a></p>
12899 <p class=flagdescription>To remain compatible with ClustalW, it is possible to
12900 indicate the sequences with this flag</p>
12902 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12903 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12904 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12905 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12907 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12908 -infile=sample_seq1.fasta </p>
12912 <p class=Note><span style='mso-ansi-language:EN-US'>Note: Common multiple sequence
12913 alignments format constitute a valid input format.<o:p></o:p></span></p>
12915 <p class=Note><span style='mso-ansi-language:EN-US'>Note: T-Coffee
12916 automatically removes the gaps </span><i><span style='mso-ansi-language:EN-US;
12917 mso-bidi-font-weight:bold'>before</span></i><span style='mso-ansi-language:
12918 EN-US'> doing the alignment. This behaviour is different from that of ClustalW
12919 where the gaps are kept.<o:p></o:p></span></p>
12921 <p class=flag><a name="_Toc101065235"></a><a name="_Toc102494766"></a><a
12922 name="_Toc151732279"><span style='mso-bookmark:_Toc102494766'><span
12923 style='mso-bookmark:_Toc101065235'><span lang=AF>-in</span></span><span
12924 lang=AF> (Cf –in from the Method and Library Input section)</span></span></a></p>
12926 <p class=flag><a name="_Toc101065236"></a><a name="_Toc102494767"></a><a
12927 name="_Toc151732280"><span style='mso-bookmark:_Toc102494767'><span
12928 style='mso-bookmark:_Toc101065236'><span lang=AF>-get_type</span></span></span></a></p>
12930 <p class=flagusage><span lang=FR>Usage: -get_type</span></p>
12932 <p class=instruction>Default: turned off</p>
12934 <p class=flagdescription>Forces t_coffee to identify the sequences type
12935 (PROTEIN, DNA).</p>
12937 <p class=flag><a name="_Toc101065237"></a><a name="_Toc102494768"></a><a
12938 name="_Toc151732281"><span style='mso-bookmark:_Toc102494768'><span
12939 style='mso-bookmark:_Toc101065237'><span lang=AF>-type [cw]</span></span></span></a></p>
12941 <p class=flagusage><span lang=FR>Usage: -type=DNA ¦ PROTEIN¦ DNA_PROTEIN</span></p>
12943 <p class=instruction>Default: -type=<automatically set></p>
12945 <p class=flagdescription>This flag sets the type of the sequences. If omitted,
12946 the type is guessed automatically. This flag is compatible with ClustalW.</p>
12948 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
12949 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
12951 <p class=Warning>Warning:<span style="mso-spacerun: yes"> </span>In case
12952 of low complexity or short sequences, it is recommended to set the type
12953 manually.<a name="_Toc101065238"></a></p>
12957 <p class=flag><span style='mso-bookmark:_Toc101065238'><a name="_Toc102494769"></a><a
12958 name="_Toc151732282"><span style='mso-bookmark:_Toc102494769'><span lang=AF>-seq</span></span></a></span></p>
12960 <p class=flagusage><span lang=FR>Usage: -seq=[<P,S><name>,]</span></p>
12962 <p class=instruction>Default: none</p>
12964 <p class=MyNormal><span lang=AF>-seq is now the recommended flag to provide
12965 your sequences. It behaves mostly like the -in flag.</span></p>
12967 <p class=flag><a name="_Toc101065239"></a><a name="_Toc102494770"></a><a
12968 name="_Toc151732283"><span style='mso-bookmark:_Toc102494770'><span
12969 style='mso-bookmark:_Toc101065239'><span lang=AF>-seq_source</span></span></span></a></p>
12971 <p class=flagusage><span lang=FR>Usage: -seq_source=<ANY or<span
12972 style="mso-spacerun: yes"> </span>_LS or LS ></span></p>
12974 <p class=instruction>Default: ANY.</p>
12976 <p class=flagdescription>You may not want to combine all the provided sequences
12977 into a single sequence list. You can do by specifying that you do not want to
12978 treat all the –in files as potential sequence sources.</p>
12980 <p class=flagdescription>-seq_source=_LA indicates that neither sequences
12981 provided via the A (Alignment) flag or via the L (Library flag) should be added
12982 to the sequence list.</p>
12984 <p class=flagdescription>-seq_source=S means that only sequences provided via
12985 the S tag will be considered. All the other sequences will be ignored.</p>
12987 <p class=Note><span style='mso-ansi-language:EN-US'>Note:<span
12988 style="mso-spacerun: yes"> </span>This flag is mostly designed for
12989 interactions between T-Coffee and T-CoffeeDPA (the large scale version of
12990 T-Coffee).</span><span style='mso-ansi-language:EN-US;mso-bidi-font-weight:
12991 bold'><o:p></o:p></span></p>
12993 <h3><a name="_Toc101065241"></a><a name="_Toc102494366"></a><a
12994 name="_Toc102494771"></a><a name="_Toc151732284"><span style='mso-bookmark:
12995 _Toc102494771'><span style='mso-bookmark:_Toc102494366'><span style='mso-bookmark:
12996 _Toc101065241'>Structure Input</span></span></span></a></h3>
12998 <p class=flag><a name="_Toc101065242"></a><a name="_Toc102494772"></a><a
12999 name="_Toc151732285"><span style='mso-bookmark:_Toc102494772'><span
13000 style='mso-bookmark:_Toc101065242'><span lang=AF>-pdb</span></span></span></a></p>
13002 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13003 </span>-pdb=<pdbid1>,<pdbid2>
\85[Max 200]</span></p>
13005 <p class=instruction>Default: None</p>
13007 <p class=flagdescription>Reads or fetch a pdb file. It is possible to specify a
13008 chain or even a sub-chain:</p>
13010 <p class=example2>PDBID(PDB_CHAIN)[opt] (FIRST,LAST)[opt]<a name="_Toc101065243"></a></p>
13012 <p class=flagdescription><span style='mso-bookmark:_Toc101065243'>It is also
13013 possible to input structures via the –in flag. In that case, you will
13014 need to use the TAG identifier:</span></p>
13016 <p class=example2><span style='mso-bookmark:_Toc101065243'>-in Ppdb1 Ppdb2
\85 </span></p>
13018 <h3><span style='mso-bookmark:_Toc101065243'><a name="_Toc102494367"></a><a
13019 name="_Toc102494773"></a><a name="_Toc151732286"><span style='mso-bookmark:
13020 _Toc102494773'><span style='mso-bookmark:_Toc102494367'>Tree Input</span></span></a></span></h3>
13022 <p class=flag><a name="_Toc101065244"></a><a name="_Toc102494774"></a><a
13023 name="_Toc151732287"><span style='mso-bookmark:_Toc102494774'><span
13024 style='mso-bookmark:_Toc101065244'><span lang=AF>-usetree</span></span></span></a></p>
13026 <p class=flagusage><span lang=FR>Usage: -usetree=<tree file></span></p>
13028 <p class=instruction>Default: No file specified</p>
13030 <p class=instruction>Format: newick tree format (ClustalW Style)</p>
13032 <p class=flagdescription>This flag indicates that rather than computing a new
13033 dendrogram, t_coffee must use a pre-computed one. The tree files are in phylips
13034 format and compatible with ClustalW. In most cases, using a pre-computed tree
13035 will halve the computation time required by t_coffee. It is also possible to
13036 use trees output by ClustalW, Phylips and any other program.</p>
13038 <h3><a name="_Toc101065245"></a><a name="_Toc102494368"></a><a
13039 name="_Toc102494775"></a><a name="_Toc151732288"><span style='mso-bookmark:
13040 _Toc102494775'><span style='mso-bookmark:_Toc102494368'><span style='mso-bookmark:
13041 _Toc101065245'>Structures, Sequences Methods and Library Input</span></span></span>
13042 via the </a><span style='mso-bookmark:_Toc151732288'><span style='font-family:
13043 Symbol;mso-ascii-font-family:"Arial Black"'>-</span>in Flag</span></h3>
13045 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
13046 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
13048 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
13049 style='text-align:center;background:#FFFF89'><a name="_Toc101065246"><span
13050 style='font-size:20.0pt;mso-bidi-font-size:10.0pt'>The -in Flag and its
13051 Identifier TAGS<o:p></o:p></span></a></p>
13053 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13054 style='mso-bookmark:_Toc101065246'><o:p> </o:p></span></p>
13056 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13057 style='mso-bookmark:_Toc101065246'><-in> is the real grinder of T-Coffee.
13058 Sequences, methods and alignments all pass through so that T-Coffee can turn it
13059 all into a single list of constraints (the library). Everything is done
13060 automatically with T-Coffee going through each file to extract the sequences it
13061 contains. The methods are then applied to the sequences. Pre-compiled
13062 constraint list can also be provided. Each file provided via this flag must be
13063 preceded with a symbol (Identifier TAG) that indicates its nature to T-Coffee.
13064 The TAGs currently supported are the following:</span></p>
13066 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13067 style='mso-bookmark:_Toc101065246'><o:p> </o:p></span></p>
13069 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13070 style='mso-bookmark:_Toc101065246'>P<span style='mso-tab-count:1'> </span>PDB
13071 structure</span></p>
13073 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13074 style='mso-bookmark:_Toc101065246'>S <span style='mso-tab-count:1'> </span>for
13075 sequences (use it as well to treat an MSA as unaligned sequences)</span></p>
13077 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13078 style='mso-bookmark:_Toc101065246'><o:p> </o:p></span></p>
13080 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13081 style='mso-bookmark:_Toc101065246'>M <span style='mso-tab-count:1'> </span>Methods
13082 used to build the library</span></p>
13084 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13085 style='mso-bookmark:_Toc101065246'>L <span style='mso-tab-count:1'> </span>Pre-computed
13086 T-Coffee library</span></p>
13088 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13089 style='mso-bookmark:_Toc101065246'>A <span style='mso-tab-count:1'> </span>Multiple
13090 Alignments that must be turned into a Library</span></p>
13092 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13093 style='mso-bookmark:_Toc101065246'><o:p> </o:p></span></p>
13095 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13096 style='mso-bookmark:_Toc101065246'>X <span style='mso-tab-count:1'> </span>Substitution
13097 matrices.</span></p>
13099 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13100 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13101 _Toc101065246'>R <span style='mso-tab-count:2'> </span>Profiles.
13102 This is a legal multiple alignments that will be treated as single sequences
13103 (the sequences it contains will not be realigned). </span></p>
13105 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13106 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13107 _Toc101065246'><o:p> </o:p></span></p>
13109 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13110 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13111 _Toc101065246'>If you do not want to use the TAGS, you will need to use the
13112 following flags in replacement of -in. Do not use the TAGS when using these
13115 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13116 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13117 _Toc101065246'><o:p> </o:p></span></p>
13119 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13120 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13121 _Toc101065246'>-aln <span style='mso-tab-count:3'> </span>Alignments
13122 <span style='mso-tab-count:1'> </span>(A)</span></p>
13124 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13125 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13126 _Toc101065246'>-profile<span style='mso-tab-count:1'> </span>Profiles
13127 <span style='mso-tab-count:1'> </span>(R)</span></p>
13129 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13130 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13131 _Toc101065246'>-method<span style='mso-tab-count:1'> </span>Method
13132 <span style='mso-tab-count:1'> </span>(M)</span></p>
13134 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13135 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13136 _Toc101065246'>-seq<span style='mso-tab-count:3'> </span>Sequences
13137 <span style='mso-tab-count:1'> </span>(S)</span></p>
13139 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13140 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13141 _Toc101065246'>-lib<span style='mso-tab-count:3'> </span>Libraries<span
13142 style='mso-tab-count:1'> </span>(L)<a
13143 name="_Toc102494776"></a></span></p>
13147 <p class=flag><span style='mso-bookmark:_Toc101065246'><span style='mso-bookmark:
13148 _Toc102494776'><a name="_Toc151732289"><span lang=AF>-in</span></a></span></span></p>
13150 <p class=flagusage><span lang=FR>Usage: -in=[<P,S,A,L,M,X><name>,]</span></p>
13152 <p class=instruction>Default: -in=Mlalign_id_pair,Mclustalw_pair</p>
13154 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
13155 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
13157 <p class=Warning>Note: -in can be replaced with the combined usage of -aln,
13158 iprofile, .pdb, .lib, -method.</p>
13162 <p class=flagdescription>See the box for an explanation of the -in flag. The
13163 following argument passed via -in</p>
13165 <p class=flagdescription><o:p> </o:p></p>
13167 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13168 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13169 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13170 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13172 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13173 -in=Ssample_seq1.fasta,Asample_aln1.aln,Asample_aln2.msf,Mlalign_id_pair,Lsample_lib1.tc_lib
13174 –outfile=outaln</p>
13178 <p class=flagdescription><o:p> </o:p></p>
13180 <p class=flagdescription>This command will trigger the following chain of
13183 <p class=flagdescription><o:p> </o:p></p>
13185 <p class=flagdescription>1-Gather all the sequences</p>
13187 <p class=flagdescription>Sequences within all the provided files are pooled
13188 together. Format recognition is automatic. Duplicates are removed (if they have
13189 the same name). Duplicates in a single file are only tolerated in FASTA format
13190 file, although they will cause sequences to be renamed.</p>
13192 <p class=flagdescription>In the above case, the total set of sequences will be
13193 made of sequences contained in sequences1.seq, alignment1.aln, alignment2.msf
13194 and library.lib, plus the sequences initially gathered<span
13195 style="mso-spacerun: yes"> </span>by -infile.</p>
13197 <p class=flagdescription>2-Turn alignments into libraries</p>
13199 <p class=flagdescription>alignment1.aln and alignment2.msf will be read and
13200 turned into libraries. Another library will be produced by applying the method
13201 lalign_id_pair to the set of sequences previously obtained (1). The final
13202 library used for the alignment will be the combination of all this information.
13205 <p class=flagdescription>Note as well the following rules: </p>
13207 <p class=flagdescription><o:p> </o:p></p>
13209 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>1-Order</b><span
13210 style='mso-bidi-font-weight:bold'>:</span> The order in which sequences,
13211 methods, alignments and libraries are fed in is irrelevant.</p>
13213 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>2-Heterogeneity</b><span
13214 style='mso-bidi-font-weight:bold'>:</span> There is no need for each element
13215 (A, S, L) to contain the same sequences.</p>
13217 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>3-No Duplicate</b><span
13218 style='mso-bidi-font-weight:bold'>:</span> Each file should contain only one
13219 copy of each sequence. Duplicates are only allowed in FASTA files but will
13220 cause the sequences to be renamed.</p>
13222 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>4-Reconciliation</b><span
13223 style='mso-bidi-font-weight:bold'>:</span> If two files (for instance two
13224 alignments) contain different versions of the same sequence due to an indel, a
13225 new sequence will be reconstructed and used instead:</p>
13227 <p class=example2CxSpFirst>aln 1:hgab1 <span style='mso-tab-count:1'> </span>AAAAABAAAAA</p>
13229 <p class=example2CxSpLast>aln 2:hgab1<span style='mso-tab-count:1'> </span>AAAAAAAAAACCC</p>
13231 <p class=flagdescription>will cause the program to reconstruct and use the
13232 following sequence </p>
13234 <p class=example2>hgab1<span style='mso-tab-count:1'> </span>AAAAABAAAAACCC
13237 <p class=flagdescription>This can be useful if you are trying to combine
13238 several runs of blast, or structural information where residues may have been
13239 deleted. However substitutions are forbidden. If two sequences with the same
13240 name cannot be merged, they will cause the program to exit with an information
13243 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>5-Methods</b><span
13244 style='mso-bidi-font-weight:bold'>:</span> The method describer can either be
13245 built in (See ### for a list of all the available methods) or be a file
13246 describing the method to be used. The exact syntax is provided in part 4 of
13249 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>6-Substitution
13250 Matrices</b><span style='mso-bidi-font-weight:bold'>: </span>If the method is a
13251 substitution matrix (X) then no other type of information should be provided.
13254 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13255 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13256 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13257 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13259 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13260 sample_seq1.fasta -in=Xpam250mt<span style="mso-spacerun: yes">
13261 </span>-gapopen=-10<span style="mso-spacerun: yes"> </span>-gapext=-1 </p>
13265 <p class=flagdescription>This command results in a progressive alignment
13266 carried out on the sequences in seqfile. The procedure does not use any more
13267 the T-Coffee concistency based algorithm, but switches to a standard
13268 progressive alignment algorithm (like ClustalW or Pileup) much less accurate.
13269 In this context, appropriate gap penalties should be provided. The matrices are
13270 in the file source/matrices.h. Add-Hoc matrices can also be provided by the
13271 user (see the matrices format section at the end of this manual).</p>
13273 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
13274 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
13276 <p class=Warning>Warning: Xmatrix does not have the same effect as using the
13277 -matrix flag.<span style="mso-spacerun: yes"> </span>The -matrix defines
13278 the matrix that will be used while compiling the library while the Xmatrix
13279 defines the matrix used when assembling the final alignment.</p>
13283 <h3><a name="_Toc101065247"></a><a name="_Toc102494369"></a><a
13284 name="_Toc102494777"></a><a name="_Toc151732290"><span style='mso-bookmark:
13285 _Toc102494777'><span style='mso-bookmark:_Toc102494369'><span style='mso-bookmark:
13286 _Toc101065247'>Profile Input</span></span></span></a></h3>
13288 <p class=flag><a name="_Toc101065248"></a><a name="_Toc102494778"></a><a
13289 name="_Toc151732291"><span style='mso-bookmark:_Toc102494778'><span
13290 style='mso-bookmark:_Toc101065248'><span lang=AF>-profile</span></span></span></a></p>
13292 <p class=flagusage><span lang=FR>Usage: -profile=[<name>,] maximum of 200
13293 profiles.</span></p>
13295 <p class=instruction>Default: no default</p>
13297 <p class=flagdescription>This flag causes T-Coffee to treat multiple alignments
13298 as a single sequences, thus making it possible to make multiple profile alignments.
13299 The profile-profile alignment is controlled by <span style='mso-bidi-font-weight:
13300 bold'>-profile_mode</span> and <span style='mso-bidi-font-weight:bold'>-profile_comparison</span>.
13301 When provided with the <b style='mso-bidi-font-weight:normal'>-in</b> flag,
13302 profiles must be preceded with the letter R.</p>
13304 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13305 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13306 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13307 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13309 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13310 –profile sample_aln1.aln,sample_aln2.aln –outfile=profile_aln</p>
13312 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13313 –in Rsample_aln1.aln,Rsample_aln2.aln,Mslow_pair,Mlalign_id_pair
13314 –outfile=profile_aln</p>
13318 <p class=flagdescription>Note that when using –template_file, the program
13319 will also look for the templates associated with the profiles, even if the
13320 profiles have been provided as templates themselves (however it will not look
13321 for the template of the profile templates of the profile templates
\85)</p>
13323 <p class=flag><a name="_Toc101065249"></a><a name="_Toc102494779"></a><a
13324 name="_Toc151732292"><span style='mso-bookmark:_Toc102494779'><span
13325 style='mso-bookmark:_Toc101065249'><span lang=AF>-profile1 [cw]</span></span></span></a></p>
13327 <p class=flagusage><span lang=FR>Usage: -profile1=[<name>], one name only</span></p>
13329 <p class=instruction>Default: no default</p>
13331 <p class=flagdescription>Similar to the previous one and was provided for
13332 compatibility with ClustalW.</p>
13334 <p class=flag><a name="_Toc101065250"></a><a name="_Toc102494780"></a><a
13335 name="_Toc151732293"><span style='mso-bookmark:_Toc102494780'><span
13336 style='mso-bookmark:_Toc101065250'><span lang=AF>-profile2 [cw]</span></span></span></a></p>
13338 <p class=flagusage><span lang=FR>Usage: -profile1=[<name>], one name only</span></p>
13340 <p class=instruction>Default: no default</p>
13342 <p class=flagdescription>Similar to the previous one and was provided for
13343 compatibility with ClustalW.</p>
13345 <h2><a name="_Toc101065251"></a><a name="_Toc102494370"></a><a
13346 name="_Toc102494781"></a><a name="_Toc151732294"><span style='mso-bookmark:
13347 _Toc102494781'><span style='mso-bookmark:_Toc102494370'><span style='mso-bookmark:
13348 _Toc101065251'>Alignment Computation</span></span></span></a></h2>
13350 <h3><a name="_Toc101065252"></a><a name="_Toc102494371"></a><a
13351 name="_Toc102494782"></a><a name="_Toc151732295"><span style='mso-bookmark:
13352 _Toc102494782'><span style='mso-bookmark:_Toc102494371'><span style='mso-bookmark:
13353 _Toc101065252'>Library Computation: Methods</span></span></span></a></h3>
13355 <p class=flag><a name="_Toc102494783"></a><a name="_Toc151732296"><span
13356 style='mso-bookmark:_Toc102494783'><span lang=AF>-lalign_n_top</span></span></a></p>
13358 <p class=flagusage><span lang=FR>Usage: -lalign_n_top=<Integer></span></p>
13360 <p class=instruction>Default: -lalign_n_top=10</p>
13362 <p class=flagdescription>Number of alignment reported by the local method
13365 <p class=flag><a name="_Toc102494784"></a><a name="_Toc151732297"><span
13366 style='mso-bookmark:_Toc102494784'><span lang=AF>-align_pdb_param_file</span></span></a></p>
13368 <p class=flagdescription>Unsuported</p>
13370 <p class=flag><a name="_Toc102494785"></a><a name="_Toc151732298"><span
13371 style='mso-bookmark:_Toc102494785'><span lang=AF>-align_pdb_hasch_mode</span></span></a></p>
13373 <p class=flagdescription>Unsuported<a name="_Toc101065253"></a></p>
13375 <h3><span style='mso-bookmark:_Toc101065253'><a name="_Toc102494372"></a><a
13376 name="_Toc102494786"></a><a name="_Toc151732299"><span style='mso-bookmark:
13377 _Toc102494786'><span style='mso-bookmark:_Toc102494372'>Library Computation:
13378 Extension</span></span></a></span></h3>
13380 <p class=flag><a name="_Toc101065255"></a><a name="_Toc101065254"></a><a
13381 name="_Toc102494787"></a><a name="_Toc151732300"><span style='mso-bookmark:
13382 _Toc102494787'><span style='mso-bookmark:_Toc101065254'><span style='mso-bookmark:
13383 _Toc101065255'><span lang=AF>-</span></span></span><span style='mso-bookmark:
13384 _Toc101065255'><span lang=AF>lib_list [Unsupported]</span></span></span></a><span
13385 style='mso-bookmark:_Toc101065255'></span></p>
13387 <p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=FR>Usage:<span
13388 style="mso-spacerun: yes"> </span>-lib_list=<filename> </span></span></p>
13390 <p class=instruction><span style='mso-bookmark:_Toc101065255'>Default:unset</span></p>
13392 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'>Use this flag
13393 if you do not want the library computation to take into account all the
13394 possible pairs in your dataset. For instance</span></p>
13396 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'>Format:</span></p>
13398 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
13399 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
13400 background:#E6E6E6'>
13402 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065255'><span
13403 style='mso-tab-count:1'> </span>2 Name1 name2 </span></p>
13405 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065255'><span
13406 style='mso-tab-count:1'> </span>2 Name1 name4</span></p>
13408 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065255'><span
13409 style='mso-tab-count:1'> </span>3 Name1 Name2
13410 Name3
\85</span></p>
13414 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span
13415 style='mso-tab-count:1'> </span>(the
13416 line 3 would be used by a multiple alignment method).</span></p>
13418 <p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc102494788"></a><a
13419 name="_Toc151732301"><span style='mso-bookmark:_Toc102494788'><span lang=AF>-do_normalise</span></span></a></span></p>
13421 <p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=FR>Usage:<span
13422 style="mso-spacerun: yes"> </span>-do_normalise=<0 or a positive
13423 value> </span></span></p>
13425 <p class=instruction><span style='mso-bookmark:_Toc101065255'>Default:-do_normalise=1000</span></p>
13427 <p class=instruction><span style='mso-bookmark:_Toc101065255'>Development Only</span></p>
13429 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'>When using a
13430 value different from 0, this flag sets the score of the highest scoring pair to
13433 <p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc102494789"></a><a
13434 name="_Toc151732302"><span style='mso-bookmark:_Toc102494789'><span lang=AF>-extend</span></span></a></span></p>
13436 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13437 </span>-extend=<0,1 or a positive value> </span></p>
13439 <p class=instruction>Default:-extend=1</p>
13441 <p class=instruction>Development Only</p>
13443 <p class=flagdescription>When turned on, this flag indicates that the library
13444 extension should be carried out when performing the multiple alignment. If <b>-extend
13445 =0</b>, the extension is not made, if it is set to 1, the extension is made on
13446 all the pairs in the library. If the extension is set to another positive
13447 value, the extension is only carried out on pairs having a weight value
13448 superior to the specified limit.<a name="_Toc101065256"></a></p>
13450 <p class=flag><span style='mso-bookmark:_Toc101065256'><a name="_Toc102494790"></a><a
13451 name="_Toc151732303"><span style='mso-bookmark:_Toc102494790'><span lang=AF>-extend_mode</span></span></a></span></p>
13453 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13454 </span>-extend=<string></span></p>
13456 <p class=instruction>Default:-extend=very_fast_triplet</p>
13458 <p class=instruction>Warning: Development Only</p>
13460 <p class=flagdescription>Controls the algorithm for matrix extension. Available
13463 <p class=flagdescription>relative_triplet<span style='mso-tab-count:2'> </span>Unsupported</p>
13465 <p class=flagdescription>g_coffee<span style='mso-tab-count:3'> </span>Unsupported</p>
13467 <p class=flagdescription>g_coffee_quadruplets<span style='mso-tab-count:1'> </span>Unsupported</p>
13469 <p class=flagdescription>fast_triplet<span style='mso-tab-count:2'> </span>Fast
13470 triplet extension</p>
13472 <p class=flagdescription>very_fast_triplet<span style='mso-tab-count:2'> </span>slow
13473 triplet extension, limited to the <b>-max_n_pair</b> best sequence pairs when
13474 aligning two profiles</p>
13476 <p class=flagdescription>slow_triplet<span style='mso-tab-count:2'> </span>Exhaustive
13477 use of all the triplets</p>
13479 <p class=flagdescription>mixt<span style='mso-tab-count:3'> </span>Unsupported</p>
13481 <p class=flagdescription>quadruplet<span style='mso-tab-count:2'> </span>Unsupported</p>
13483 <p class=flagdescription>test<span style='mso-tab-count:3'> </span>Unsupported</p>
13485 <p class=flagdescription>matrix<span style='mso-tab-count:3'> </span>Use
13486 of the matrix <b>-matrix<o:p></o:p></b></p>
13488 <p class=flagdescription>fast_matrix<span style='mso-tab-count:2'> </span>Use
13489 of the matrix <b>-matrix</b>. Profiles are turned into consensus</p>
13491 <p class=flag><a name="_Toc101065257"></a><a name="_Toc102494791"></a><a
13492 name="_Toc151732304"><span style='mso-bookmark:_Toc102494791'><span
13493 style='mso-bookmark:_Toc101065257'><span lang=AF>-max_n_pair</span></span></span></a></p>
13495 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13496 </span>-max_n_pair=<integer></span></p>
13498 <p class=instruction>Default:-extend=10</p>
13500 <p class=instruction>Development Only</p>
13502 <p class=flagdescription>Controls the number of pairs considered by the <b>-extend_mode</b>=very_fast_triplet.
13503 Setting it to 0 forces all the pairs to be considered (equivalent to <b>-extend_mode</b>=slow_triplet).</p>
13505 <p class=flag><a name="_Toc101065258"></a><a name="_Toc102494792"></a><a
13506 name="_Toc151732305"><span style='mso-bookmark:_Toc102494792'><span
13507 style='mso-bookmark:_Toc101065258'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>
13509 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13510 </span>Unsupported</span></p>
13512 <p class=flag><a name="_Toc101065259"></a><a name="_Toc102494793"></a><a
13513 name="_Toc151732306"><span style='mso-bookmark:_Toc102494793'><span
13514 style='mso-bookmark:_Toc101065259'><span lang=AF>-compact</span></span></span></a></p>
13516 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13517 </span>Unsupported</span></p>
13519 <p class=flag><a name="_Toc101065260"></a><a name="_Toc102494794"></a><a
13520 name="_Toc151732307"><span style='mso-bookmark:_Toc102494794'><span
13521 style='mso-bookmark:_Toc101065260'><span lang=AF>-clean</span></span></span></a></p>
13523 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13524 </span>Unsupported</span></p>
13526 <p class=flag><a name="_Toc101065261"></a><a name="_Toc102494795"></a><a
13527 name="_Toc151732308"><span style='mso-bookmark:_Toc102494795'><span
13528 style='mso-bookmark:_Toc101065261'><span lang=AF>-maximise</span></span></span></a></p>
13530 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13531 </span>Unsupported</span></p>
13533 <p class=flag><a name="_Toc101065262"></a><a name="_Toc102494796"></a><a
13534 name="_Toc151732309"><span style='mso-bookmark:_Toc102494796'><span
13535 style='mso-bookmark:_Toc101065262'><span lang=AF>-do_self</span></span></span></a></p>
13537 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13538 </span>Flag -do_self</span></p>
13540 <p class=flagusage><span lang=FR>Default: No</span></p>
13542 <p class=flagdescription>This flag causes the extension to carried out within
13543 the sequences (as opposed to between sequences). This is necessary when looking
13544 for internal repeats with Mocca.</p>
13546 <p class=flag><a name="_Toc101065263"></a><a name="_Toc102494797"></a><a
13547 name="_Toc151732310"><span style='mso-bookmark:_Toc102494797'><span
13548 style='mso-bookmark:_Toc101065263'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>
13550 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13551 </span>Unsupported</span></p>
13553 <p class=flag><a name="_Toc101065264"></a><a name="_Toc102494798"></a><a
13554 name="_Toc151732311"><span style='mso-bookmark:_Toc102494798'><span
13555 style='mso-bookmark:_Toc101065264'><span lang=AF>-weight</span></span></span></a></p>
13557 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13558 </span>-weight=<winsimN, sim or sim_<matrix_name or matrix_file> or
13559 <integer value></span></p>
13561 <p class=instruction>Default: -weight=sim</p>
13563 <p class=flagdescription>Weight defines the way alignments are weighted when
13564 turned into a library.<span style="mso-spacerun: yes">
13565 </span>Overweighting can be obtained with the OW<X> weight mode.</p>
13567 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><o:p> </o:p></span></p>
13569 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>winsimN
13570 </span>indicates that the weight assigned to a given pair will be equal to the
13571 percent identity within a window of 2N+1 length centered on that pair. For
13572 instance winsim10 defines a window of 10 residues around the pair being
13573 considered. This gives its own weight to each residue in the output library. In
13574 our hands, this type of weighting scheme has not provided any significant
13575 improvement over the standard sim value.</p>
13577 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13578 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13579 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13580 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13582 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13583 sample_seq1.fasta -weight=winsim10 –out_lib=test.tc_lib </p>
13587 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim</span>
13588 indicates that the weight equals the average identity within the sequences
13589 containing the matched residues.</p>
13591 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>OW<X></span><span
13592 class=StyleflagdescriptionBoldItalicChar><span style='font-style:normal;
13593 mso-bidi-font-style:italic'> </span></span><span
13594 class=StyleflagdescriptionBoldItalicChar><span style='font-weight:normal;
13595 mso-bidi-font-weight:bold;font-style:normal;mso-bidi-font-style:italic'>Will
13596 cause the sim weight to be multiplied by X<o:p></o:p></span></span></p>
13598 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim_matrix_name</span>
13599 indicates the average identity with two residues regarded as identical when
13600 their substitution value is positive. The valid matrices names are in <i
13601 style='mso-bidi-font-style:normal'>matrices.h (pam250mt) .</i>Matrices not
13602 found in this header are considered to be filenames. See the format section for
13603 matrices. For instance, <i style='mso-bidi-font-style:normal'>-weight=sim_pam250mt</i>
13604 indicates that the grouping used for similarity will be the set of classes with
13605 positive substitutions. </p>
13607 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13608 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13609 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13610 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13612 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13613 sample_seq1.fasta -weight=winsim10 –out_lib=test.tc_lib </p>
13617 <p class=flagdescription>Other groups include </p>
13619 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim_clustalw_col</span><i
13620 style='mso-bidi-font-style:normal'> </i>( categories of clustalw marked with :)</p>
13622 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim_clustalw_dot</span>
13623 ( categories of clustalw marked with .)</p>
13625 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>Value</span><i
13626 style='mso-bidi-font-style:normal'> </i>indicates that all the pairs found in
13627 the alignments must be given the same weight equal to value. This is useful
13628 when the alignment one wishes to turn into a library must be given a
13629 pre-specified score (for instance if they come from a structure
13630 super-imposition program). Value is an integer:</p>
13632 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13633 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13634 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13635 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13637 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13638 sample_seq1.fasta -weight=1000 –out_lib=test.tc_lib </p>
13642 <h3><a name="_Toc101065265"></a><a name="_Toc102494373"></a><a
13643 name="_Toc102494799"></a><a name="_Toc151732312"><span style='mso-bookmark:
13644 _Toc102494799'><span style='mso-bookmark:_Toc102494373'><span style='mso-bookmark:
13645 _Toc101065265'>Tree Computation</span></span></span></a></h3>
13647 <p class=flag><a name="_Toc101065266"></a><a name="_Toc102494800"></a><a
13648 name="_Toc151732313"><span style='mso-bookmark:_Toc102494800'><span
13649 style='mso-bookmark:_Toc101065266'><span lang=AF>-</span></span></span><span
13650 lang=AF>distance_matrix_mode</span></a></p>
13652 <p class=flagusage><span lang=FR>Usage: -distance_matrix_mode=<slow, fast,
13653 very_fast></span></p>
13655 <p class=instruction>Default: very_fast</p>
13657 <p class=flagdescription>This flag indicates the method used for computing the
13658 distance matrix (distance between every pair of sequences) required for the
13659 computation of the dendrogram. </p>
13661 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>Slow</b> <span
13662 style='mso-tab-count:1'> </span>The chosen dp_mode using the extended library, </p>
13664 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>fast</b>:<span
13665 style="mso-spacerun: yes"> </span><span style='mso-tab-count:1'> </span>The
13666 fasta dp_mode using the extended library.</p>
13668 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>very_fast</b><span
13669 style='mso-tab-count:1'> </span>The
13670 fasta dp_mode using blosum62mt.</p>
13672 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>ktup<span
13673 style='mso-tab-count:1'> </span></b>Ktup matching (Muscle kind) </p>
13675 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>aln<span
13676 style='mso-tab-count:2'> </span></b>Read
13677 the distances on a precomputed MSA</p>
13679 <p class=flag><a name="_Toc101065267"></a><a name="_Toc102494801"></a><a
13680 name="_Toc151732314"><span style='mso-bookmark:_Toc102494801'><span
13681 style='mso-bookmark:_Toc101065267'><span lang=AF>-quicktree [CW]</span></span></span></a></p>
13683 <p class=flagusage><span lang=FR>Usage: -quicktree</span></p>
13685 <p class=instruction>Description: Causes T-Coffee to compute a fast approximate
13688 <p class=MyNormal><span lang=AF>This flag is kept for compatibility with
13689 ClustalW. It indicates that:</span></p>
13691 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13692 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13693 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13694 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13696 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13697 sample_seq1.fasta –distance_matrix_mode=very_fast </p>
13699 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13700 sample_seq1.fasta –quicktree </p>
13704 <h3><a name="_Toc101065268"></a><a name="_Toc102494374"></a><a
13705 name="_Toc102494802"></a><a name="_Toc151732315"><span style='mso-bookmark:
13706 _Toc102494802'><span style='mso-bookmark:_Toc102494374'><span style='mso-bookmark:
13707 _Toc101065268'>Pair-wise Alignment Computation</span></span></span></a></h3>
13709 <p class=Noteboxtitle><o:p> </o:p></p>
13711 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
13712 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
13714 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
13715 style='text-align:center;background:#FFFF89'><span style='font-size:20.0pt'>Controlling
13716 Alignment Computation<o:p></o:p></span></p>
13718 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p> </o:p></p>
13720 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>Most parameters in
13721 this section refer to the alignment mode fasta_pair_wise and cfatsa_pair_wise.
13722 When using these alignment modes, things proceed as follow:</p>
13724 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>1-Sequences are
13725 recoded using a degenerated alphabet provided with <-sim_matrix> </p>
13727 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>2-Recoded sequences
13728 are then hashed into ktuples of size <u><-ktup></u></p>
13730 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>3-Dynamic
13731 programming runs on the <u><-ndiag></u> best diagonals whose score is
13732 higher than <u><-diag_threshold></u>, the way diagonals are scored is
13733 controlled via <u><-diag_mode></u> .</p>
13735 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>4-The Dynamic
13736 computation is made to optimize either the library scoring scheme (as defined
13737 by the <u>-in</u> flag) or a substitution matrix as provided via the <u>-matrix</u>
13738 flag. The penalty scheme is defined by <u>-gapopen</u> and <u>-gapext</u>. If <u>-gapopen</u>
13739 is undefined, the value defined in <u>-cosmetic_penalty</u> is used instead.</p>
13741 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>5-Terminal gaps are
13742 scored according to <u>-tg_mode</u></p>
13746 <p class=noteboxbody><o:p> </o:p></p>
13748 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
13750 <p class=flag><a name="_Toc101065269"></a><a name="_Toc102494803"></a><a
13751 name="_Toc151732316"><span style='mso-bookmark:_Toc102494803'><span
13752 style='mso-bookmark:_Toc101065269'><span lang=AF>-dp_mode</span></span></span></a></p>
13754 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13755 </span>-dp_mode=<string></span></p>
13757 <p class=instruction>Default: -dp_mode=cfasta_fair_wise</p>
13759 <p class=flagdescription>This flag indicates the type of dynamic programming
13760 used by the program:</p>
13762 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13763 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13764 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13765 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13767 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13768 sample_seq1.fasta –dp_mode myers_miller_pair_wise </p>
13772 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>gotoh_pair_wise</span>:
13773 implementation of the gotoh algorithm (quadratic in memory and time)</p>
13775 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>myers_miller_pair_wise</span>:
13776 implementation of the Myers and Miller dynamic programming algorithm (
13777 quadratic in time and linear in space). This algorithm is recommended for very
13778 long sequences. It is about 2 times slower than gotoh and only accepts <i
13779 style='mso-bidi-font-style:normal'>tg_mode=1or 2 (i.e. gaps penalized for
13780 opening).<o:p></o:p></i></p>
13782 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>fasta_pair_wise</span><i
13783 style='mso-bidi-font-style:normal'>: </i>implementation of the fasta algorithm.
13784 The sequence is hashed, looking for <i style='mso-bidi-font-style:normal'>ktuples</i>
13785 words. Dynamic programming is only carried out on the <i style='mso-bidi-font-style:
13786 normal'>ndiag</i> best scoring diagonals. This is much faster but less accurate
13787 than the two previous. This mode is controlled by the parameters <b>-ktuple,
13788 -diag_mode and -ndiag<o:p></o:p></b></p>
13790 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>cfasta_pair_wise</span>:
13791 c stands for checked. It is the same algorithm. The dynamic programming is made
13792 on the <i style='mso-bidi-font-style:normal'>ndiag</i> best diagonals, and then
13793 on the 2*ndiags, and so on until the scores converge. Complexity will depend on
13794 the level of divergence of the sequences, but will usually be L*log(L), with an
13795 accuracy comparable to the two first mode ( this was checked on BaliBase). This
13796 mode is controlled by the parameters <b>-ktuple, -diag_mode and –ndiag<o:p></o:p></b></p>
13798 <p class=Note><span style='mso-ansi-language:EN-US'>Note: Users may find by
13799 looking into the code that other modes with fancy names exists
13800 (viterby_pair_wise
\85) Unless mentioned in this documentation, these modes are
13801 not supported.<o:p></o:p></span></p>
13803 <p class=flag><a name="_Toc101065270"></a><a name="_Toc102494804"></a><a
13804 name="_Toc151732317"><span style='mso-bookmark:_Toc102494804'><span
13805 style='mso-bookmark:_Toc101065270'><span lang=AF>-ktuple</span></span></span></a></p>
13807 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13808 </span>-ktuple=<value></span></p>
13810 <p class=instruction>Default: -ktuple=1 or 2</p>
13812 <p class=flagdescription>Indicates the ktuple size for cfasta_pair_wise dp_mode
13813 and fasta_pair_wise. It is set to 1 for proteins, and 2 for DNA. The alphabet
13814 used for protein can be a degenerated version, set with <b><u>-sim_matrix.</u></b>.
13817 <p class=flag><a name="_Toc101065271"></a><a name="_Toc102494805"></a><a
13818 name="_Toc151732318"><span style='mso-bookmark:_Toc102494805'><span
13819 style='mso-bookmark:_Toc101065271'><span lang=AF>-ndiag</span></span></span></a></p>
13821 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13822 </span>-ndiag=<value></span></p>
13824 <p class=instruction>Default: -ndiag=0</p>
13826 <p class=flagdescription>Indicates the number of diagonals used by the <i>fasta_pair_wise</i>
13827 algorithm (cf <b>-dp_mode</b>). When<span style="mso-spacerun: yes">
13828 </span><b>-ndiag=0</b>, n_diag=Log (length of the smallest sequence)+1. </p>
13830 <p class=Note><span style='mso-ansi-language:EN-US'>When –ndiag and
13831 –diag_threshold are set, diagonals are selected if and only if they
13832 fulfill both conditions.<o:p></o:p></span></p>
13834 <p class=flag><a name="_Toc101065272"></a><a name="_Toc102494806"></a><a
13835 name="_Toc151732319"><span style='mso-bookmark:_Toc102494806'><span
13836 style='mso-bookmark:_Toc101065272'><span lang=AF>-diag_mode</span></span></span></a></p>
13838 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13839 </span>-diag_mode=<value></span></p>
13841 <p class=instruction>Default: -diag_mode=0</p>
13843 <p class=flagdescription>Indicates the manner in which diagonals are scored
13844 during the fasta hashing. </p>
13846 <p class=flagdescription>0: indicates that the score of a diagonal is equal to
13847 the sum of the scores of the exact matches it contains. </p>
13849 <p class=flagdescription>1 indicates that this score is set equal to the score
13850 of the best uninterrupted segment (useful when dealing with fragments of
13853 <p class=flag><a name="_Toc101065273"></a><a name="_Toc102494807"></a><a
13854 name="_Toc151732320"><span style='mso-bookmark:_Toc102494807'><span
13855 style='mso-bookmark:_Toc101065273'><span lang=AF>-diag_threshold</span></span></span></a></p>
13857 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13858 </span>-diag_threshold=<value></span></p>
13860 <p class=instruction>Default: -diag_threshold=0</p>
13862 <p class=flagdescription>Sets the value of the threshold when selecting
13865 <p class=flagdescription>0: indicates that –ndiag should be used to
13866 select the diagonals (cf –ndiag section).</p>
13868 <p class=flag><a name="_Toc101065274"></a><a name="_Toc102494808"></a><a
13869 name="_Toc151732321"><span style='mso-bookmark:_Toc102494808'><span
13870 style='mso-bookmark:_Toc101065274'><span lang=AF>-sim_matrix</span></span></span></a></p>
13872 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13873 </span>-sim_matrix=<string></span></p>
13875 <p class=instruction>Default: -sim_matrix=vasiliky</p>
13877 <p class=flagdescription>Indicates the manner in which the amino acid alphabet
13878 is degenerated when hashing in the fasta_pairwise dynamic programming. Standard
13879 ClustalW matrices are all valid. They are used to define groups of amino acids
13880 having positive substitution values. In T-Coffee, the default is a 13 letter
13881 grouping named Vasiliky, with residues grouped as follows:</p>
13883 <p class=example2>rk, de, qh, vilm, fy (other residues kept alone).</p>
13885 <p class=flagdescription>This alphabet is set with the flag <b>-sim_matrix=vasiliky</b>.
13886 In order to keep the alphabet non degenerated, <b>-sim_matrix=idmat </b>can be
13887 used to retain the standard alphabet.</p>
13889 <p class=flag><a name="_Toc101065275"></a><a name="_Toc102494809"></a><a
13890 name="_Toc151732322"><span style='mso-bookmark:_Toc102494809'><span
13891 style='mso-bookmark:_Toc101065275'><span lang=AF>-matrix [CW]</span></span></span></a></p>
13893 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13894 </span>-matrix=<blosum62mt></span></p>
13896 <p class=instruction>Default: -matrix=blosum62mt</p>
13898 <p class=flagdescription>The usage of this flag has been modified from previous
13899 versions, due to frequent mistakes in its usage. This flag sets the matrix that
13900 will be used by alignment methods within t_coffee (slow_pair, lalign_id_pair).
13901 It does not affect external methods (like clustal_pair, clustal_aln
\85). </p>
13903 <p class=flagdescription>Users can also provide their own matrices, using the
13904 matrix format described in the appendix.</p>
13906 <p class=flag><a name="_Toc101065276"></a><a name="_Toc102494810"></a><a
13907 name="_Toc151732323"><span style='mso-bookmark:_Toc102494810'><span
13908 style='mso-bookmark:_Toc101065276'><span lang=AF>-nomatch</span></span></span></a></p>
13910 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13911 </span>-nomatch=<positive value></span></p>
13913 <p class=instruction>Default: -nomatch=0</p>
13915 <p class=flagdescription>Indicates the penalty to associate with a match. When
13916 using a library, all matches are positive or equal to 0. Matches equal to 0 are
13917 unsupported by the library but non-penalized. Setting nomatch to a non-negative
13918 value makes it possible to penalize these null matches and prevent unrelated
13919 sequences from being aligned (this can be useful when the alignments are meant
13920 to be used for structural modeling).</p>
13922 <p class=flag><a name="_Toc101065277"></a><a name="_Toc102494811"></a><a
13923 name="_Toc151732324"><span style='mso-bookmark:_Toc102494811'><span
13924 style='mso-bookmark:_Toc101065277'><span lang=AF>-gapopen</span></span></span></a></p>
13926 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13927 </span>-gapopen=<negative value></span></p>
13929 <p class=instruction>Default: -gapopen=0</p>
13931 <p class=flagdescription>Indicates the penalty applied for opening a gap. The
13932 penalty must be negative. If no value is provided when using a substitution
13933 matrix, a value will be automatically computed.</p>
13935 <p class=flagdescription>Here are some guidelines regarding the tuning of
13936 gapopen and gapext. In T-Coffee matches get a score between 0 (match) and 1000
13937 (match perfectly consistent with the library). The default cosmetic penalty is
13938 set to -50 (5% of a perfect match). If you want to tune -gapoen and see a
13939 strong effect, you should therefore consider values between 0 and -1000. </p>
13941 <p class=flag><a name="_Toc101065278"></a><a name="_Toc102494812"></a><a
13942 name="_Toc151732325"><span style='mso-bookmark:_Toc102494812'><span
13943 style='mso-bookmark:_Toc101065278'><span lang=AF>-gapext</span></span></span></a></p>
13945 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13946 </span>-gapext=<negative value></span></p>
13948 <p class=instruction>Default: -gapext=0</p>
13950 <p class=flagdescription>Indicates the penalty applied for extending a gap (cf <b><u>-gapopen</u></b>)</p>
13952 <p class=flag><a name="_Toc101065279"></a><a name="_Toc102494813"></a><a
13953 name="_Toc151732326"><span style='mso-bookmark:_Toc102494813'><span
13954 style='mso-bookmark:_Toc101065279'><span lang=AF>-fgapopen</span></span></span></a></p>
13956 <p class=flagusage><span lang=FR>Unsupported</span></p>
13958 <p class=flag><a name="_Toc101065280"></a><a name="_Toc102494814"></a><a
13959 name="_Toc151732327"><span style='mso-bookmark:_Toc102494814'><span
13960 style='mso-bookmark:_Toc101065280'><span lang=AF>-fgapext</span></span></span></a></p>
13962 <p class=flagusage><span lang=FR>Unsupported</span></p>
13964 <p class=flag><a name="_Toc101065281"></a><a name="_Toc102494815"></a><a
13965 name="_Toc151732328"><span style='mso-bookmark:_Toc102494815'><span
13966 style='mso-bookmark:_Toc101065281'><span lang=AF>-cosmetic_penalty</span></span></span></a></p>
13968 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13969 </span>-cosmetic_penalty=<negative value></span></p>
13971 <p class=instruction>Default: -cosmetic_penalty=-50</p>
13973 <p class=flagdescription>Indicates the penalty applied for opening a gap. This
13974 penalty is set to a very low value. It will only have an influence on the
13975 portions of the alignment that are unalignable. It will not make them more
13976 correct, but only more pleasing to the eye ( i.e. Avoid stretches of lonely
13979 <p class=flagdescription>The cosmetic penalty is automatically turned off if a
13980 substitution matrix is used rather than a library.</p>
13982 <p class=flag><a name="_Toc101065282"></a><a name="_Toc102494816"></a><a
13983 name="_Toc151732329"><span style='mso-bookmark:_Toc102494816'><span
13984 style='mso-bookmark:_Toc101065282'><span lang=AF>-tg_mode</span></span></span></a></p>
13986 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
13987 </span>-tg_mode=<0, 1, or 2></span></p>
13989 <p class=instruction>Default: -tg_mode=1</p>
13991 <p class=flagdescription>0: terminal gaps penalized with <span
13992 class=StyleflagdescriptionBoldItalicChar>-gapopen + -gapext*len<o:p></o:p></span></p>
13994 <p class=flagdescription>1: terminal gaps penalized with a <span
13995 class=StyleflagdescriptionBoldItalicChar>-gapext*len<o:p></o:p></span></p>
13997 <p class=flagdescription>2: terminal gaps unpenalized.</p>
13999 <p class=flagdescription><o:p> </o:p></p>
14001 <h3><a name="_Toc101065283"></a><a name="_Toc102494375"></a><a
14002 name="_Toc102494817"></a><a name="_Toc151732330"><span style='mso-bookmark:
14003 _Toc102494817'><span style='mso-bookmark:_Toc102494375'><span style='mso-bookmark:
14004 _Toc101065283'>Weighting Schemes</span></span></span></a></h3>
14006 <p class=flag><a name="_Toc101065284"></a><a name="_Toc102494818"></a><a
14007 name="_Toc151732331"><span style='mso-bookmark:_Toc102494818'><span
14008 style='mso-bookmark:_Toc101065284'><span lang=AF>-seq_weight</span></span></span></a></p>
14010 <p class=flagusage><span lang=FR>Usage: -seq_weight=<t_coffee or
14011 <file_name>></span></p>
14013 <p class=instruction>Default: -seq_weight=t_coffee</p>
14015 <p class=flagdescription>These are the individual weights assigned to each
14016 sequence. The t_coffee weights try to compensate the bias in consistency caused
14017 by redundancy in the sequences.</p>
14019 <p class=Formula><span style='mso-tab-count:1'> </span>sim(A,B)=%similarity
14020 between A and B, between 0 and 1. </p>
14022 <p class=Formula><span style='mso-tab-count:1'> </span>weight(A)=1/sum(sim(A,X)^3)</p>
14024 <p class=flagdescription>Weights are normalized so that their sum equals the
14025 number of sequences. They are applied onto the primary library in the following
14028 <p class=Formula><span style='mso-tab-count:1'> </span>res_score(Ax,By)=Min(weight(A),
14029 weight(B))*res_score(Ax, By)</p>
14031 <p class=flagdescription>These are very simple weights. Their main goal is to
14032 prevent a single sequence present in many copies to dominate the alignment.</p>
14034 <p class=Note><span style='mso-ansi-language:EN-US'>Note: The library output by
14035 -out_lib is the un-weighted<span style="mso-spacerun: yes">
14036 </span>library. <o:p></o:p></span></p>
14038 <p class=Note><span style='mso-ansi-language:EN-US'>Note: Weights can be output
14039 using the -outseqweight flag.<o:p></o:p></span></p>
14041 <p class=Note><span style='mso-ansi-language:EN-US'>Note: You can use your own
14042 weights (see the format section). <o:p></o:p></span></p>
14044 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
14046 <h3><a name="_Toc101065285"></a><a name="_Toc102494376"></a><a
14047 name="_Toc102494819"></a><a name="_Toc151732332"><span style='mso-bookmark:
14048 _Toc102494819'><span style='mso-bookmark:_Toc102494376'><span style='mso-bookmark:
14049 _Toc101065285'>Multiple Alignment Computation</span></span></span></a></h3>
14051 <p class=flag><a name="_Toc101065286"></a><a name="_Toc102494820"></a><a
14052 name="_Toc151732333"><span style='mso-bookmark:_Toc102494820'><span
14053 style='mso-bookmark:_Toc101065286'><span lang=AF>-msa_mode</span></span></span></a></p>
14055 <p class=flagusage><span lang=FR>Usage:
14056 -msa_mode=<tree,graph,precomputed></span></p>
14058 <p class=instruction>Default: -evaluate_mode=tree</p>
14060 <p class=flagdescription>Unsupported</p>
14062 <p class=flag><a name="_Toc101065287"></a><a name="_Toc102494821"></a><a
14063 name="_Toc151732334"><span style='mso-bookmark:_Toc102494821'><span
14064 style='mso-bookmark:_Toc101065287'><span lang=AF>-one2all</span></span></span></a><span
14065 style='mso-bookmark:_Toc102494821'><span style='mso-bookmark:_Toc101065287'></span></span></p>
14067 <p class=flagusage><span style='mso-bookmark:_Toc102494821'><span
14068 style='mso-bookmark:_Toc101065287'><span lang=FR>Usage: -one2all=<name></span></span></span></p>
14070 <p class=instruction><span style='mso-bookmark:_Toc102494821'><span
14071 style='mso-bookmark:_Toc101065287'>Default: not used</span></span></p>
14073 <p class=flagdescription><span style='mso-bookmark:_Toc102494821'><span
14074 style='mso-bookmark:_Toc101065287'>Will generate a one to all library with
14075 respect to the specified sequence and will then align all the sequences in turn
14076 to that sequence, in a sequence determined by the order in which the sequences
14077 were provided.<span style="mso-spacerun: yes"> </span></span></span></p>
14079 <p class=flagdescription><span style='mso-bookmark:_Toc102494821'><span
14080 style='mso-bookmark:_Toc101065287'><b style='mso-bidi-font-weight:normal'>–profile_comparison
14081 =profile</b>, the MSAs provided via –profile are vectorized and the
14082 function specified by –profile_comparison is used to make profile profile
14083 alignments. In that case, the complexity is NL^2</span></span></p>
14085 <p class=flag><span style='mso-bookmark:_Toc102494821'><span style='mso-bookmark:
14086 _Toc101065287'><a name="_Toc151732335"><span lang=AF>-profile</span></a></span></span><span
14087 style='mso-bookmark:_Toc151732335'><span lang=AF>_comparison</span></span></p>
14089 <p class=flagusage><span lang=FR>Usage: -profile_mode=<fullN,profile></span></p>
14091 <p class=instruction>Default: -profile_mode=full50</p>
14093 <p class=flagdescription>The profile mode flag controls the multiple profile
14094 alignments in T-Coffee. There are two instances where t_coffee can make
14095 multiple profile alignments:</p>
14097 <p class=flagdescription>1-When N, the number of sequences is higher than <b
14098 style='mso-bidi-font-weight:normal'>–maxnseq, </b>the program switches to
14099 its multiple profile alignment mode (t_coffee_dpa).</p>
14101 <p class=flagdescription>2-When MSAs are provided via the <b style='mso-bidi-font-weight:
14102 normal'>–profile</b> flag or via <b style='mso-bidi-font-weight:normal'>–profile1</b>
14103 and <b style='mso-bidi-font-weight:normal'>–profile2</b>. </p>
14105 <p class=flagdescription>In these situations, the –profile_mode value
14106 influences the alignment computation, these values are:</p>
14108 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>–profile_comparison
14109 =profile</b>, the MSAs provided via –profile are vectorized and the
14110 function specified by –profile_comparison is used to make profile profile
14111 alignments. In that case, the complexity is NL^2</p>
14113 <p class=flagdescription><span class=ListChar><b style='mso-bidi-font-weight:
14114 normal'><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt'>-profile_comparison=fullN</span></b></span>,
14115 N is an integer value that can omitted. <i style='mso-bidi-font-style:normal'>Full</i>
14116 indicates that given two profiles, the alignment will be based on a library
14117 that includes every possible pair of sequences between the two profiles. If N
14118 is set, then the library will be restricted to the N most similar pairs of
14119 sequences between the two profiles, as judged from a measure made on a pairwise
14120 alignment of these two profiles.</p>
14122 <p class=flag><a name="_Toc101065288"></a><a name="_Toc102494822"></a><a
14123 name="_Toc151732336"><span style='mso-bookmark:_Toc102494822'><span
14124 style='mso-bookmark:_Toc101065288'><span lang=AF>-profile_</span></span></span><span
14125 lang=AF>mode</span></a></p>
14127 <p class=flagusage><span lang=FR>Usage: -profile_mode=<cw_profile_profile,
14128 muscle_profile_profile, multi_channel></span></p>
14130 <p class=instruction>Default: -profile_mode=cw_profile_profile</p>
14132 <p class=flagdescription>When <b style='mso-bidi-font-weight:normal'>–profile_comparison=profile</b>,
14133 this flag selects a profile scoring function.</p>
14135 <h3><a name="_Toc101065289"></a><a name="_Toc102494377"></a><a
14136 name="_Toc102494823"></a><a name="_Toc151732337"><span style='mso-bookmark:
14137 _Toc102494823'><span style='mso-bookmark:_Toc102494377'><span style='mso-bookmark:
14138 _Toc101065289'>Alignment Post-Processing</span></span></span></a></h3>
14140 <p class=flag><a name="_Toc101065290"></a><a name="_Toc102494824"></a><a
14141 name="_Toc151732338"><span style='mso-bookmark:_Toc102494824'><span
14142 style='mso-bookmark:_Toc101065290'><span lang=AF>-clean_aln</span></span></span></a></p>
14144 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
14145 </span>-clean_aln<span style="mso-spacerun: yes"> </span></span></p>
14147 <p class=instruction>Default:-clean_aln</p>
14149 <p class=flagdescription>This flag causes T-Coffee to post-process the multiple
14150 alignment. Residues that have a reliability score smaller or equal to
14151 -clean_threshold (as given by an evaluation that uses
14152 -clean_evaluate_mode)<span style="mso-spacerun: yes"> </span>are
14153 realigned to the rest of the alignment. Residues with a score higher than the
14154 threshold constitute a rigid framework that cannot be altered.</p>
14156 <p class=flagdescription>The cleaning algorithm is greedy. It starts from the
14157 top left segment of low constituency residues and works its way left to right,
14158 top to bottom along the alignment. You can require this operation to be carried
14159 out for several cycles using the -clean_iterations flag.</p>
14161 <p class=flagdescription>The rationale behind this operation is mostly
14162 cosmetic. In order to ensure a decent looking alignment, the gop is set to -20
14163 and the gep to -1. There is no penalty for terminal gaps, and the matrix is
14166 <p class=Note><span style='mso-ansi-language:EN-US'>Note: Gaps are always
14167 considered to have a reliability score of 0.<o:p></o:p></span></p>
14169 <p class=Note><span class=WarningChar>Note: The use of the cleaning option can
14170 result in memory overflow when aligning large</span><span style='mso-ansi-language:
14171 EN-US'> </span><span class=WarningChar>sequences,<o:p></o:p></span></p>
14173 <p class=flag><a name="_Toc101065291"></a><a name="_Toc102494825"></a><a
14174 name="_Toc151732339"><span style='mso-bookmark:_Toc102494825'><span
14175 style='mso-bookmark:_Toc101065291'><span lang=AF>-clean_threshold</span></span></span></a></p>
14177 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
14178 </span>-clean_threshold=<0-9><span style="mso-spacerun: yes">
14181 <p class=flagusage><span lang=FR>Default:-clean_aln=1</span></p>
14183 <p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>
14185 <p class=flag><a name="_Toc101065292"></a><a name="_Toc102494826"></a><a
14186 name="_Toc151732340"><span style='mso-bookmark:_Toc102494826'><span
14187 style='mso-bookmark:_Toc101065292'><span lang=AF>-clean_iteration</span></span></span></a></p>
14189 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
14190 </span>-clean_iteration=<value between 1 and ><span style="mso-spacerun:
14191 yes"> </span></span></p>
14193 <p class=instruction>Default:-clean_iteration=1</p>
14195 <p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>
14197 <p class=flag><a name="_Toc101065293"></a><a name="_Toc102494827"></a><a
14198 name="_Toc151732341"><span style='mso-bookmark:_Toc102494827'><span
14199 style='mso-bookmark:_Toc101065293'><span lang=AF>-clean_evaluation_mode</span></span></span></a></p>
14201 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
14202 </span>-clean_iteration=<evaluation_mode ><span style="mso-spacerun:
14203 yes"> </span></span></p>
14205 <p class=instruction>Default:-clean_iteration=t_coffee_non_extended</p>
14207 <p class=flagdescription>Indicates the mode used for the evaluation that will
14208 indicate the segments that should be realigned. See -evaluation_mode for the
14209 list of accepted modes.</p>
14211 <p class=flag><a name="_Toc101065294"></a><a name="_Toc102494828"></a><a
14212 name="_Toc151732342"><span style='mso-bookmark:_Toc102494828'><span
14213 style='mso-bookmark:_Toc101065294'><span lang=AF>-iterate</span></span></span></a></p>
14215 <p class=flagusage><span lang=FR>Usage: -iterate=<integer></span></p>
14217 <p class=instruction>Default: -iterate=0</p>
14219 <p class=flagdescription>Sequences are extracted in turn and realigned to the
14220 MSA. If iterate is set to -1, each sequence is realigned, otherwise the number
14221 of iterations is set by –iterate.</p>
14223 <h2><a name="_Toc101065295"></a><a name="_Toc102494378"></a><a
14224 name="_Toc102494829"></a><a name="_Toc151732343"><span style='mso-bookmark:
14225 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14226 _Toc101065295'>BLAST Template Selection Parameters</span></span></span></a><span
14227 style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span
14228 style='mso-bookmark:_Toc101065295'></span></span></span></h2>
14230 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494829'><span
14231 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>These
14232 parameters are used by T-Coffee when running expresso, accurate and psicoffee</span></span></span></p>
14234 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14235 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732344"><span
14236 lang=AF>-blast_server</span></a><span lang=AF> </span></span></span></span></p>
14238 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14239 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14240 style='mso-ansi-language:EN-US'>Usage:<span style="mso-spacerun: yes">
14241 </span>-blast_server=</span> <span lang=FR>EBI, NCBI or LOCAL_BLAST</span></span></span></span><span
14242 style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span
14243 style='mso-bookmark:_Toc101065295'><span style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></p>
14245 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14246 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14247 EBI</span></span></span></p>
14249 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14250 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14251 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Defines whih way BLAST
14252 will be used<o:p></o:p></span></span></span></span></p>
14254 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14255 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732345"><span
14256 lang=AF>-prot_min_sim</span></a><span lang=AF> </span></span></span></span></p>
14258 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14259 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14260 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-prot_min_sim= <percent_id></span></span></span></span></p>
14262 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14263 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14264 40</span></span></span></p>
14266 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14267 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14268 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum id for inclusion
14269 of a sequence in a psi-blast profile<o:p></o:p></span></span></span></span></p>
14271 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14272 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732346"><span
14273 lang=AF>-prot_max_sim</span></a><span lang=AF> </span></span></span></span></p>
14275 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14276 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14277 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-prot_max_sim= <percent_id></span></span></span></span></p>
14279 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14280 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14281 90</span></span></span></p>
14283 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14284 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14285 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Maximum id for inclusion
14286 of a sequence in a psi-blast profile.<o:p></o:p></span></span></span></span></p>
14288 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14289 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732347"><span
14290 lang=AF>-prot_min_cov</span></a><span lang=AF> </span></span></span></span></p>
14292 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14293 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14294 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-prot_min_cov= <percent></span></span></span></span></p>
14296 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14297 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14298 40</span></span></span></p>
14300 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14301 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14302 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum coverage for
14303 inclusion of a sequence in a psi-blast profile<o:p></o:p></span></span></span></span></p>
14305 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14306 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732348"><span
14307 lang=AF>-protein_db</span></a><span lang=AF> </span></span></span></span></p>
14309 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14310 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14311 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-protein_db= <BLAST
14312 database></span></span></span></span></p>
14314 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14315 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14316 nr</span></span></span></p>
14318 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14319 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14320 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Database used for
14321 construction of psi-blast profiles</span></span></span></span></p>
14323 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14324 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732349"><span
14325 lang=AF>-pdb_min_sim</span></a><span lang=AF> </span></span></span></span></p>
14327 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14328 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14329 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-pdb_min_sim= <percent_id></span></span></span></span></p>
14331 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14332 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14333 35</span></span></span></p>
14335 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14336 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14337 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum id for a PDB
14338 template to be selected by expresso<o:p></o:p></span></span></span></span></p>
14340 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14341 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732350"><span
14342 lang=AF>-pdb_max_sim</span></a><span lang=AF> </span></span></span></span></p>
14344 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14345 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14346 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-pdb_max_sim= <percent_id></span></span></span></span></p>
14348 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14349 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14350 100</span></span></span></p>
14352 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14353 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14354 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Maximum id for a PDB
14355 template to be selected by expresso <o:p></o:p></span></span></span></span></p>
14357 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14358 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732351"><span
14359 lang=AF>-pdb_min_cov</span></a><span lang=AF> </span></span></span></span></p>
14361 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14362 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14363 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-pdb_min_cov= <percent></span></span></span></span></p>
14365 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14366 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14367 50</span></span></span></p>
14369 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14370 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14371 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum coverage for a
14372 PDB template to be selected by expresso. <o:p></o:p></span></span></span></span></p>
14374 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14375 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732352"><span
14376 lang=AF>-pdb_db</span></a><span lang=AF> </span></span></span></span></p>
14378 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14379 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14380 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-protein_db= <BLAST
14381 database></span></span></span></span></p>
14383 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14384 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14385 pdb</span></span></span></p>
14387 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14388 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14389 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Database for PDB
14390 template to be selected by expresso.</span></span></span></span></p>
14392 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14393 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732353"><span
14394 lang=AF>-pdb_type</span></a><span lang=AF> </span></span></span></span></p>
14396 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14397 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14398 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-pdb_type= d,n,m,dnm,dn</span></span></span></span></p>
14400 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14401 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14402 d</span></span></span></p>
14404 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14405 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14406 _Toc101065295'><span style='mso-bidi-font-weight:bold'>d: diffraction<o:p></o:p></span></span></span></span></p>
14408 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14409 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14410 _Toc101065295'><span style='mso-bidi-font-weight:bold'>n: NMR<o:p></o:p></span></span></span></span></p>
14412 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14413 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14414 _Toc101065295'><span style='mso-bidi-font-weight:bold'>m: model</span></span></span></span></p>
14416 <h2><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span
14417 style='mso-bookmark:_Toc101065295'><a name="_Toc151732354">CPU Control</a></span></span></span></h2>
14419 <h3><a name="_Toc101065296"></a><a name="_Toc102494379"></a><a
14420 name="_Toc102494830"></a><a name="_Toc151732355"><span style='mso-bookmark:
14421 _Toc102494830'><span style='mso-bookmark:_Toc102494379'><span style='mso-bookmark:
14422 _Toc101065296'>Multithreading</span></span></span></a></h3>
14424 <p class=flag><a name="_Toc101065297"></a><a name="_Toc102494831"></a><a
14425 name="_Toc151732356"><span style='mso-bookmark:_Toc102494831'><span
14426 style='mso-bookmark:_Toc101065297'><span lang=AF>-multi_core</span></span></span></a><span
14427 style='mso-bookmark:_Toc102494831'><span style='mso-bookmark:_Toc101065297'><span
14428 lang=AF> </span></span></span></p>
14430 <p class=flagusage><span style='mso-ansi-language:EN-US'>Usage:<span
14431 style="mso-spacerun: yes"> </span>-multi_core=</span><span lang=FR>
14432 templates_jobs_relax_msa</span><span style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
14434 <p class=instruction>Default: 0</p>
14436 <p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
14437 bold'>template: </span>fetch the templates in a parallel way</p>
14439 <p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
14440 bold'>jobs:</span> compute the library</p>
14442 <p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
14443 bold'>relax:</span> extend the library in a parallel way</p>
14445 <p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
14446 bold'>msa:</span> compute the msa in a parallel way</p>
14448 <p class=instruction><o:p> </o:p></p>
14450 <p class=flagdescription>Specifies that the steps of T-Coffee that should be
14451 multi threaded. by default all relevant steps are parallelized.</p>
14453 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14454 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14455 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14456 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14458 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14459 sample_seq2.fasta -multi_core jobs</p>
14463 <p class=flagdescription><a name="_Toc101065298"></a><a name="_Toc102494380"></a><a
14464 name="_Toc102494832"><span style='mso-bookmark:_Toc102494380'><span
14465 style='mso-bookmark:_Toc101065298'>In order to prevent the use of the parallel
14466 mode it is possible to use:</span></span></a></p>
14468 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14469 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14470 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14471 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14473 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
14474 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14475 style='mso-bookmark:_Toc101065298'>PROMPT: t_coffee sample_seq2.fasta
14476 -multi_core no</span></span></span></p>
14480 <p class=flag><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:
14481 _Toc102494380'><span style='mso-bookmark:_Toc101065298'><span lang=AF><o:p> </o:p></span></span></span></span></p>
14483 <p class=flag><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:
14484 _Toc102494380'><span style='mso-bookmark:_Toc101065298'><a name="_Toc151732357"><span
14485 lang=AF>-n_core</span></a><span lang=AF> </span></span></span></span></p>
14487 <p class=flagusage><span style='mso-bookmark:_Toc102494832'><span
14488 style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc101065298'><span
14489 style='mso-ansi-language:EN-US'>Usage:<span style="mso-spacerun: yes">
14490 </span>-n_core=</span> <span lang=FR><number of cores></span></span></span></span><span
14491 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14492 style='mso-bookmark:_Toc101065298'><span style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></p>
14494 <p class=instruction><span style='mso-bookmark:_Toc102494832'><span
14495 style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc101065298'>Default:
14496 0</span></span></span></p>
14498 <p class=flagdescription><span style='mso-bookmark:_Toc102494832'><span
14499 style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc101065298'>Default
14500 indicates that all cores will be used, as indicated by the environment via:</span></span></span></p>
14502 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14503 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14504 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14505 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14507 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
14508 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14509 style='mso-bookmark:_Toc101065298'>PROMPT: t_coffee sample_seq2.fasta -multi_core
14510 jobs</span></span></span></p>
14514 <h3><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14515 style='mso-bookmark:_Toc101065298'><o:p> </o:p></span></span></span></h3>
14517 <h3><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14518 style='mso-bookmark:_Toc101065298'><a name="_Toc151732358">Limits</a></span></span></span></h3>
14520 <p class=flag><a name="_Toc101065299"></a><a name="_Toc102494833"></a><a
14521 name="_Toc151732359"><span style='mso-bookmark:_Toc102494833'><span
14522 style='mso-bookmark:_Toc101065299'><span lang=AF>-mem_mode</span></span></span></a></p>
14524 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
14525 </span>deprecated</span><span lang=FR style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>
14527 <p class=flag><a name="_Toc101065300"></a><a name="_Toc102494834"></a><a
14528 name="_Toc151732360"><span style='mso-bookmark:_Toc102494834'><span
14529 style='mso-bookmark:_Toc101065300'><span lang=AF>-ulimit</span></span></span></a></p>
14531 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
14532 </span>-ulimit=<value></span></p>
14534 <p class=instruction>Default: -ulimit=0</p>
14536 <p class=flagdescription>Specifies the upper limit of memory usage (in
14537 Megabytes). Processes exceeding this limit will automatically exit. A value 0
14538 indicates that no limit applies.</p>
14540 <p class=flag><a name="_Toc101065301"></a><a name="_Toc102494835"></a><a
14541 name="_Toc151732361"><span style='mso-bookmark:_Toc102494835'><span
14542 style='mso-bookmark:_Toc101065301'><span lang=AF>-maxlen</span></span></span></a></p>
14544 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
14545 </span>-maxlen=<value, 0=nolimit></span></p>
14547 <p class=instruction>Default: -maxlen=1000<span style='mso-bidi-font-weight:
14548 bold'><o:p></o:p></span></p>
14550 <p class=flagdescription>Indicates the maximum length of the sequences. <a
14551 name="_Toc101065302"></a></p>
14553 <h3><span style='mso-bookmark:_Toc101065302'><a name="_Toc102494381"></a><a
14554 name="_Toc102494836"></a><a name="_Toc151732362"><span style='mso-bookmark:
14555 _Toc102494836'><span style='mso-bookmark:_Toc102494381'>Aligning more than 100
14556 sequences with DPA</span></span></a></span></h3>
14558 <p class=flag><a name="_Toc101065303"></a><a name="_Toc102494837"></a><a
14559 name="_Toc151732363"><span style='mso-bookmark:_Toc102494837'><span
14560 style='mso-bookmark:_Toc101065303'><span lang=AF>-maxnseq</span></span></span></a></p>
14562 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
14563 </span>-maxnseq=<value, 0=nolimit></span></p>
14565 <p class=instruction>Default: -maxnseq=50</p>
14567 <p class=flagdescription>Indicates the maximum number of sequences before
14568 triggering the use of t_coffee_dpa.</p>
14570 <p class=flag><a name="_Toc101065304"></a><a name="_Toc102494838"></a><a
14571 name="_Toc151732364"><span style='mso-bookmark:_Toc102494838'><span
14572 style='mso-bookmark:_Toc101065304'><span lang=AF>-dpa_master_aln</span></span></span></a></p>
14574 <p class=flagusage><span lang=FR>Usage: -dpa_master_aln=<File, method></span></p>
14576 <p class=instruction>Default: -dpa_master_aln=NO</p>
14578 <p class=flagdescription>When using dpa, t_coffee needs a seed alignment that
14579 can be computed using any appropriate method. By default, t_coffee computes a
14580 fast approximate alignment.</p>
14582 <p class=flagdescription>A pre-alignment can be provided through this flag, as
14583 well as any program using the following syntax:</p>
14585 <p class=example2>your_script –in <fasta_file> -out
14586 <file_name></p>
14588 <p class=flag><a name="_Toc101065305"></a><a name="_Toc102494839"></a><a
14589 name="_Toc151732365"><span style='mso-bookmark:_Toc102494839'><span
14590 style='mso-bookmark:_Toc101065305'><span lang=AF>-dpa_maxnseq</span></span></span></a></p>
14592 <p class=flagusage><span lang=FR>Usage: -dpa_maxnseq=<integer value></span></p>
14594 <p class=instruction>Default: -dpa_maxnseq=30</p>
14596 <p class=flagdescription>Maximum number of sequences aligned simultaneously
14597 when DPA is ran. Given the tree computed from the master alignment, a node is
14598 sent to computation if it controls more than <b style='mso-bidi-font-weight:
14599 normal'>–dpa_maxnseq</b> OR if it controls a pair of sequences having
14600 less than <b style='mso-bidi-font-weight:normal'>–dpa_min_score2</b>
14601 percent ID.<a name="_Toc101065306"></a></p>
14603 <p class=flag><span style='mso-bookmark:_Toc101065306'><a name="_Toc102494840"></a><a
14604 name="_Toc151732366"><span style='mso-bookmark:_Toc102494840'><span lang=AF>-dpa_min_score1</span></span></a></span></p>
14606 <p class=flagusage><span lang=FR>Usage: -dpa_min_score1=<integer value></span></p>
14608 <p class=instruction>Default: -dpa_min_score1=95</p>
14610 <p class=flagdescription>Threshold for not realigning the sequences within the
14611 master alignment. Given this alignment and the associated tree, sequences below
14612 a node are not realigned if none of them has less than<b style='mso-bidi-font-weight:
14613 normal'> –dpa_min_score1</b> % identity.<a name="_Toc101065307"></a></p>
14615 <p class=flag><span style='mso-bookmark:_Toc101065307'><a name="_Toc102494841"></a><a
14616 name="_Toc151732367"><span style='mso-bookmark:_Toc102494841'><span lang=AF>-dpa_min_score2</span></span></a></span></p>
14618 <p class=flagusage><span lang=FR>Usage: -dpa_min_score2</span></p>
14620 <p class=instruction>Default: -dpa_min_score2</p>
14622 <p class=flagdescription>Maximum number of sequences aligned simultaneously
14623 when DPA is ran. Given the tree computed from the master alignment, a node is
14624 sent to computation if it controls more than <b style='mso-bidi-font-weight:
14625 normal'>–dpa_maxnseq</b> OR if it controls a pair of sequences having
14626 less than <b style='mso-bidi-font-weight:normal'>–dpa_min_score2</b>
14627 percent ID.<a name="_Toc101065308"></a></p>
14629 <p class=flag><span style='mso-bookmark:_Toc101065308'><a name="_Toc102494842"></a><a
14630 name="_Toc151732368"><span style='mso-bookmark:_Toc102494842'><span lang=AF>-dap_tree
14631 [NOT IMPLEMENTED]</span></span></a></span></p>
14633 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
14634 </span>-dpa_tree=<filename></span></p>
14636 <p class=instruction>Default: -unset</p>
14638 <p class=flagdescription>Guide tree used in DPA. This is a newick tree where
14639 the distance associated with each node is set to the minimum pairwise distance
14640 among all considered sequences.</p>
14642 <h2><a name="_Toc101065309"></a><a name="_Toc102494382"></a><a
14643 name="_Toc102494843"></a><a name="_Toc151732369"><span style='mso-bookmark:
14644 _Toc102494843'><span style='mso-bookmark:_Toc102494382'><span style='mso-bookmark:
14645 _Toc101065309'>Using Structures</span></span></span></a><a name="_Toc101065310"></a></h2>
14647 <h3><span style='mso-bookmark:_Toc101065310'><a name="_Toc102494383"></a><a
14648 name="_Toc102494844"></a><a name="_Toc151732370"><span style='mso-bookmark:
14649 _Toc102494844'><span style='mso-bookmark:_Toc102494383'>Generic</span></span></a></span></h3>
14651 <p class=flag><a name="_Toc151732371"><span lang=AF>-mode</span></a></p>
14653 <p class=flagusage><span lang=FR>Usage: -mode=3dcoffee</span></p>
14655 <p class=instruction>Default: turned off</p>
14657 <p class=flagdescription>Runs t_coffee with the 3dcoffee mode (cf next
14660 <p class=flag><a name="_Toc101065312"></a><a name="_Toc102494846"></a><a
14661 name="_Toc151732372"><span style='mso-bookmark:_Toc102494846'><span
14662 style='mso-bookmark:_Toc101065312'><span lang=AF>-check_pdb_status</span></span></span></a></p>
14664 <p class=flagusage><span lang=FR>Usage: -check_pdb_status</span></p>
14666 <p class=instruction>Default: turned off</p>
14668 <p class=flagdescription>Forces t_coffee to run extract_from_pdb to check the
14669 pdb status of each sequence. This can considerably slow down the program.</p>
14671 <p class=flagdescription><o:p> </o:p></p>
14673 <h3><a name="_Toc101065313"></a><a name="_Toc102494384"></a><a
14674 name="_Toc102494847"></a><a name="_Toc151732373"><span style='mso-bookmark:
14675 _Toc102494847'><span style='mso-bookmark:_Toc102494384'><span style='mso-bookmark:
14676 _Toc101065313'>3D Coffee: Using SAP</span></span></span></a></h3>
14678 <p class=flagdescription>It is possible to use t_coffee to compute multiple structural
14679 alignments. To do so, ensure that you have the sap program installed.</p>
14681 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14682 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14683 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14684 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14686 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14687 –pdb=struc1.pdb,struc2.pdb,struc3.pdb -method sap_pair</p>
14691 <p class=flagdescription>Will combine the pairwise alignments produced by
14692 SAP.<span style="mso-spacerun: yes"> </span>There are currently four
14693 methods that can be interfaced with t_coffee:</p>
14695 <p class=flagdescription>sap_pair: that uses the sap algorithm</p>
14697 <p class=flagdescription>align_pdb: uses a t_coffee implementation of sap, not
14700 <p class=flagdescription>tmaliagn_pair
14701 (http://zhang.bioinformatics.ku.edu/TM-align/)</p>
14703 <p class=flagdescription>mustang_pair (http://www.cs.mu.oz.au/~arun/mustang)</p>
14705 <p class=flagdescription>When providing a PDB file, the computation is only
14706 carried out on the first chain of this file. If your original file contains
14707 several chain, you should extract the chain you want to work on. You can use <b
14708 style='mso-bidi-font-weight:normal'>t_coffee –other_pg extract_from_pdb </b>or
14709 any pdb handling program.</p>
14711 <p class=flagdescription>If you are working with public PDB files, you can use
14712 the PDB identifier and specify the chain by adding its index to the identifier
14713 (i.e. 1pdbC). If your structure is an NMR structure, you are advised to provide
14714 the program with one structure only.</p>
14716 <p class=flagdescription>If you wish to align only a portion of the structure,
14717 you should extract it yourself from the pdb file, using <b style='mso-bidi-font-weight:
14718 normal'>t_coffee –other_pg extract_from_pdb </b>or any pdb handling
14721 <p class=flagdescription>You can provide t_coffee with a mixture of sequences
14722 and structure. In this case, you should use the special mode:</p>
14724 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14725 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14726 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14727 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14729 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14730 –mode 3dcoffee –seq 3d_sample3.fasta -template_file
14731 template_file.template</p>
14735 <h3><a name="_Toc101065314"></a><a name="_Toc102494385"></a><a
14736 name="_Toc102494848"></a><a name="_Toc151732374"><span style='mso-bookmark:
14737 _Toc102494848'><span style='mso-bookmark:_Toc102494385'><span style='mso-bookmark:
14738 _Toc101065314'>Using/finding PDB templates for the Sequences</span></span></span></a></h3>
14740 <p class=flag><a name="_Toc101065315"></a><a name="_Toc102494849"></a><a
14741 name="_Toc151732375"><span style='mso-bookmark:_Toc102494849'><span
14742 style='mso-bookmark:_Toc101065315'><span lang=AF>-template_file</span></span></span></a></p>
14744 <p class=flagusage><span lang=FR style='mso-bidi-font-weight:bold'>Usage</span><span
14745 lang=FR>: -template_file =</span></p>
14747 <p class=flagusage><span lang=FR><filename, </span></p>
14749 <p class=flagusage><span lang=FR>SCRIPT_scriptame, </span></p>
14751 <p class=flagusage><span lang=FR>SELF_TAG </span></p>
14753 <p class=flagusage><span lang=FR>SEQFILE_TAG_filename,</span></p>
14755 <p class=flagusage><span lang=FR>no></span></p>
14757 <p class=instruction>Default: no</p>
14759 <p class=flagdescription>This flag instructs t_coffee on the templates that
14760 will be used when combining several types of information. For instance, when
14761 using structural information, this file will indicate the structural template
14762 that corresponds to your sequences. The identifier T indicates that the file
14763 should be a FASTA like file, formatted as follows. There are several ways to
14764 pass the templates:</p>
14766 <p class=flagheading2>Predefined Modes</p>
14768 <p class=MyNormaBoldl><span lang=AF>EXPRESSO: will use the EBI server to find
14769 _P_ templates</span></p>
14771 <p class=MyNormaBoldl><span lang=AF>PSIBLAST: will use the EBI sever to find
14772 profiles </span></p>
14774 <p class=MyNormaBoldl><span lang=AF><o:p> </o:p></span></p>
14776 <p class=flagheading2>File name</p>
14778 <p class=flagdescription>This file contains the sequence/template association
14779 it uses a FASTA-like format, as follows:</p>
14781 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
14782 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
14783 background:#E6E6E6'>
14785 <p class=examplefileCxSpFirst>><sequence name> _P_ <pdb
14788 <p class=examplefileCxSpMiddle>><sequence name> _G_ <gene
14791 <p class=examplefileCxSpMiddle>><sequence name> _R_ <MSA
14794 <p class=examplefileCxSpMiddle>><sequence name> _F_ <RNA Secondary
14797 <p class=examplefileCxSpMiddle>><sequence name> _T_ <Transmembrane
14798 Secondary Structure></p>
14800 <p class=examplefileCxSpMiddle>><sequence name> _E_ <Protein
14801 Secondary Structure></p>
14803 <p class=examplefileCxSpLast><o:p> </o:p></p>
14807 <p class=flagdescription>Each template will be used in place of the sequence
14808 with the appropriate method. For instance, structural templates will be aligned
14809 with sap_pair and the information thus generated will be transferred onto the
14812 <p class=flagdescription>Note the following rule:</p>
14814 <p class=flagdescription><span style='mso-tab-count:1'> </span>-Each
14815 sequence can have one template of each type (structural, genomics
\85)</p>
14817 <p class=flagdescription><span style='mso-tab-count:1'> </span>-Each
14818 sequence can only have one template of a given type</p>
14820 <p class=flagdescription><span style='mso-tab-count:1'> </span>-Several
14821 sequences can share the same template</p>
14823 <p class=flagdescription><span style='mso-tab-count:1'> </span>-All
14824 the sequences do not need to have a template</p>
14826 <p class=flagdescription>The type of template on which a method works is
14827 declared with the SEQ_TYPE parameter in the method configuration file:</p>
14829 <p class=flagdescription><span style='mso-tab-count:1'> </span>SEQ_TYPE<span
14830 style='mso-tab-count:1'> </span>S: a method
14831 that uses sequences </p>
14833 <p class=flagdescription><span style='mso-tab-count:1'> </span>SEQ_TYPE<span
14834 style='mso-tab-count:1'> </span>PS: a
14835 pairwise method that aligns sequences and structures</p>
14837 <p class=flagdescription><span style='mso-tab-count:1'> </span>SEQ_TYPE<span
14838 style='mso-tab-count:1'> </span>P: a method
14839 that aligns structures (sap for instance)</p>
14841 <p class=flagdescription>There are 4 tags identifying the template type:</p>
14843 <p class=flagdescription>_P_<span style='mso-tab-count:1'> </span>Structural
14844 templates: a pdb identifier OR a pdb file</p>
14846 <p class=flagdescription>_G_<span style='mso-tab-count:1'> </span>Genomic
14847 templates: a protein sequence where boundary amino-acid have been recoded with
14848 ( o:0, i:1, j:2)</p>
14850 <p class=flagdescription>_R_<span style='mso-tab-count:1'> </span>Profile
14851 Templates: a file containing a multiple sequence alignment</p>
14853 <p class=flagdescription>_F_<span style='mso-tab-count:1'> </span>RNA
14854 secondary Structures</p>
14856 <p class=flagdescription><o:p> </o:p></p>
14858 <p class=flagdescription>More than one template file can be provided. There is
14859 no need to have one template for every sequence in the dataset. </p>
14861 <p class=flagdescription>_P_, _G_, and _R_ are known as <b style='mso-bidi-font-weight:
14862 normal'>template TAGS<o:p></o:p></b></p>
14864 <p class=flagheading2>2-SCRIPT_<scriptname></p>
14866 <p class=flagdescription>Indicates that filename is a script that will be used
14867 to generate a valid template file. The script will run on a file containing all
14868 your sequences using the following syntax:</p>
14870 <p class=example2>scriptname –infile=<your sequences>
14871 -outfile=<template_file></p>
14873 <p class=flagdescription>It is also possible to pass some parameters, use @ as
14874 a separator and # in place of the = sign. For instance, if you want to call the
14875 a script named blast.pl with the foloowing parameters;</p>
14877 <p class=example2>blast.pl -db=pdb -dir=/local/test</p>
14879 <p class=flagdescription>Use</p>
14881 <p class=example2>SCRIPT_blast.pl@db#pdb@dir#/local/test</p>
14883 <p class=flagdescription>Bear in mind that the input output flags will then be
14884 concatenated to this command line so that t_coffee ends up calling the program
14885 using the following system call:</p>
14887 <p class=example2>blast.pl -db=pdb -dir=/local/test -infile=<some tmp
14888 file> -outfile=<another tmp file></p>
14890 <p class=flagdescription><o:p> </o:p></p>
14892 <p class=flagheading2>3-SELF_TAG</p>
14894 <p class=flagdescription>TAG can take the value of any of the known TAGS (_S_,
14895 _G_, _P_). SELF indicates that the original name of the sequence will be used to
14896 fetch the template: </p>
14898 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14899 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14900 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14901 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14903 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14904 3d_sample2.fasta –template_file SELF_P_</p>
14908 <p class=flagdescription>The previous command will work because the sequences
14909 in 3d_sample3 are named </p>
14911 <p class=flagheading2>4-SEQFILE_TAG_filename</p>
14913 <p class=flagdescription>Use this flag if your templates are in filename, and
14914 are named according to the sequences. For instance, if your protein sequences
14915 have been recoded with Exon/Intron information, you should have the recoded
14916 sequences names according to the original:</p>
14918 <p class=example2>SEQFILE_G_recodedprotein.fasta<span style='mso-tab-count:
14921 <p class=flag><a name="_Toc101065316"></a><a name="_Toc102494850"></a><a
14922 name="_Toc151732376"><span style='mso-bookmark:_Toc102494850'><span
14923 style='mso-bookmark:_Toc101065316'><span lang=AF>-struc_to_use</span></span></span></a></p>
14925 <p class=flagusage><span lang=FR>Usage: -struc_to_use=<struc1, struc2
\85></span></p>
14927 <p class=instruction>Default: -struc_to_use=NULL</p>
14929 <p class=flagdescription>Restricts the 3Dcoffee to a set of pre-defined
14932 <h2><a name="_Toc101065317"></a><a name="_Toc102494386"></a><a
14933 name="_Toc102494851"></a><a name="_Toc151732377"><span style='mso-bookmark:
14934 _Toc102494851'><span style='mso-bookmark:_Toc102494386'><span style='mso-bookmark:
14935 _Toc101065317'>Multiple Local Alignments</span></span></span></a></h2>
14937 <p class=MyNormal><span lang=AF>It is possible to compute multiple local
14938 alignments, using the moca routine. MOCA is a routine that allows extracting
14939 all the local alignments that show some similarity with another predefined
14940 fragment.</span></p>
14942 <p class=MyNormal><span lang=AF>'mocca' is a perl script that calls t-coffee
14943 and provides it with the appropriate parameters.</span></p>
14945 <p class=flag><a name="_Toc101065318"></a><a name="_Toc102494852"></a><a
14946 name="_Toc151732378"><span style='mso-bookmark:_Toc102494852'><span
14947 style='mso-bookmark:_Toc101065318'><span lang=AF>-domain</span></span><span
14948 lang=AF>/-mocca</span></span></a></p>
14950 <p class=flagusage><span lang=FR>Usage: -domain</span></p>
14952 <p class=instruction>Default: not set</p>
14954 <p class=flagdescription>This flag indicates that t_coffee will run using the
14955 domain mode. All the sequences will be concatenated, and the resulting sequence
14956 will be compared to itself using lalign_rs_s_pair mode (lalign of the sequence
14957 against itself using keeping the lalign raw score). This step is the most
14958 computer intensive, and it is advisable to save the resulting file.</p>
14960 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14961 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14962 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14963 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14965 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14966 -in Ssample_seq1.fasta,Mlalign_rs_s_pair -out_lib=sample_lib1.mocca_lib -domain
14967 -start=100 -len=50 </p>
14971 <p class=flagdescription>This instruction will use the fragment 100-150 on the
14972 concatenated sequences, as a template for the extracted repeats. The extraction
14973 will only be made once. The library will be placed in the file <lib
14976 <p class=flagdescription><o:p> </o:p></p>
14978 <p class=flagdescription>If you want, you can test other coordinates for the
14979 repeat, such as </p>
14981 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14982 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14983 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14984 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14986 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14987 -in sample_lib1.mocca_lib -domain -start=100 -len=60 </p>
14991 <p class=flagdescription>This run will use the fragment 100-160, and will be
14992 much faster because it does not need to re-compute the lalign library. </p>
14994 <p class=flag><a name="_Toc101065319"></a><a name="_Toc102494853"></a><a
14995 name="_Toc151732379"><span style='mso-bookmark:_Toc102494853'><span
14996 style='mso-bookmark:_Toc101065319'><span lang=AF>-start</span></span></span></a></p>
14998 <p class=flagusage><span lang=FR>Usage: -start=<int value></span></p>
15000 <p class=instruction>Default: not set</p>
15002 <p class=flagdescription>This flag indicates the starting position of the
15003 portion of sequence that will be used as a template for the repeat extraction.
15004 The value assumes that all the sequences have been concatenated, and is given
15005 on the resulting sequence.</p>
15007 <p class=flag><a name="_Toc101065320"></a><a name="_Toc102494854"></a><a
15008 name="_Toc151732380"><span style='mso-bookmark:_Toc102494854'><span
15009 style='mso-bookmark:_Toc101065320'><span lang=AF>-len</span></span></span></a></p>
15011 <p class=flagusage><span lang=FR>Usage: -len=<int value></span></p>
15013 <p class=instruction>Default: not set</p>
15015 <p class=flagdescription>This flag indicates the length of the portion of
15016 sequence that will be used as a template.</p>
15018 <p class=flag><a name="_Toc101065321"></a><a name="_Toc102494855"></a><a
15019 name="_Toc151732381"><span style='mso-bookmark:_Toc102494855'><span
15020 style='mso-bookmark:_Toc101065321'><span lang=AF>-scale</span></span></span></a></p>
15022 <p class=flagusage><span lang=FR>Usage: -scale=<int value></span></p>
15024 <p class=instruction>Default: -scale=-100</p>
15026 <p class=flagdescription>This flag indicates the value of the threshold for
15027 extracting the repeats. The actual threshold is equal to:</p>
15029 <p class=flagdescription><span style='mso-tab-count:1'> </span>motif_len*scale</p>
15031 <p class=flagdescription>Increase the scale <span style='font-family:Wingdings;
15032 mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
15033 mso-char-type:symbol;mso-symbol-font-family:Wingdings'><span style='mso-char-type:
15034 symbol;mso-symbol-font-family:Wingdings'>ó</span></span>Increase sensitivity <span
15035 style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
15036 mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
15037 Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>ó</span></span>
15038 More alignments( i.e. -50).</p>
15040 <p class=flag><a name="_Toc101065322"></a><a name="_Toc102494856"></a><a
15041 name="_Toc151732382"><span style='mso-bookmark:_Toc102494856'><span
15042 style='mso-bookmark:_Toc101065322'><span lang=AF>-domain_interactive [Examples]</span></span></span></a></p>
15044 <p class=flagusage><span lang=FR>Usage: -domain_interactive</span></p>
15046 <p class=instruction>Default: unset</p>
15048 <p class=flagdescription>Launches an interactive mocca session.</p>
15050 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15051 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15052 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15053 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15055 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15056 -in Lsample_lib3.tc_lib,Mlalign_rs_s_pair -domain -start=100 -len=60</p>
15060 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
15061 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
15062 background:#E6E6E6;margin-left:0cm;margin-right:1.0cm'>
15064 <p class=examplefilesmallCxSpFirst>TOLB_ECOLI_212_26<span style='mso-tab-count:
15065 3'> </span><span
15066 style="mso-spacerun: yes"> </span>211 SKLAYVTFESGR--SALVIQTLANGAVRQV-ASFPRHNGAPAFSPDGSKLAFA</p>
15068 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_165_218<span
15069 style="mso-spacerun: yes"> </span>164
15070 TRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYV</p>
15072 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_256_306<span
15073 style="mso-spacerun: yes"> </span>255
15074 SKLAFALSKTGS--LNLYVMDLASGQIRQV-TDGRSNNTEPTWFPDSQNLAFT</p>
15076 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_307_350<span
15077 style="mso-spacerun: yes"> </span>306 -------DQAGR--PQVYKVNINGGAPQRI-TWEGSQNQDADVSSDGKFMVMV</p>
15079 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_351_393<span
15080 style="mso-spacerun: yes"> </span>350
15081 -------SNGGQ--QHIAKQDLATGGV-QV-LSSTFLDETPSLAPNGTMVIYS<span style="mso-spacerun:
15082 yes"> </span></p>
15084 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15085 yes">
15086 </span>1<span style="mso-spacerun:
15087 yes"> </span>*<span
15088 style="mso-spacerun:
15089 yes">
15090 </span>*<span style="mso-spacerun: yes"> </span>:<span
15091 style="mso-spacerun: yes">
15092 </span>.<span style="mso-spacerun: yes"> </span>.:.<span
15093 style="mso-spacerun: yes"> </span>:<span style="mso-spacerun:
15094 yes"> </span></p>
15096 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15098 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15099 yes"> </span>MENU: Type Letter
15100 Flag[number] and Return: ex |10</p>
15102 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15103 yes"> </span>|x<span
15104 style="mso-spacerun: yes"> </span>-->Set<span
15105 style="mso-spacerun: yes"> </span>the START to x</p>
15107 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15108 yes"> </span>>x<span
15109 style="mso-spacerun: yes"> </span>-->Set<span
15110 style="mso-spacerun: yes"> </span>the LEN<span
15111 style="mso-spacerun: yes"> </span>to x</p>
15113 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15114 yes"> </span>Cx<span
15115 style="mso-spacerun: yes"> </span>-->Set<span
15116 style="mso-spacerun: yes"> </span>the sCale to x</p>
15118 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15119 yes"> </span>Sname<span
15120 style="mso-spacerun: yes"> </span>-->Save<span
15121 style="mso-spacerun: yes"> </span>the<span
15122 style="mso-spacerun: yes"> </span>Alignment </p>
15124 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15125 yes"> </span>Bx<span
15126 style="mso-spacerun: yes"> </span>-->Save<span
15127 style="mso-spacerun: yes"> </span>Goes back x it </p>
15129 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15130 yes"> </span>return<span
15131 style="mso-spacerun: yes"> </span>-->Compute the<span
15132 style="mso-spacerun: yes"> </span>Alignment</p>
15134 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15135 yes"> </span>X<span
15136 style="mso-spacerun: yes">
15137 </span>-->eXit</p>
15139 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15141 <p class=examplefilesmallCxSpMiddle>[ITERATION<span style="mso-spacerun:
15142 yes"> </span>1] [START=211] [LEN= 50] [SCALE=-100]<span
15143 style="mso-spacerun: yes"> </span>YOUR CHOICE:</p>
15145 <p class=examplefilesmallCxSpMiddle>For instance, to set the length of the
15146 domain to 40, type: </p>
15148 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15150 <p class=examplefilesmallCxSpMiddle>[ITERATION<span style="mso-spacerun:
15151 yes"> </span>1] [START=211] [LEN= 50] [SCALE=-100]<span
15152 style="mso-spacerun: yes"> </span>YOUR
15153 CHOICE:>40[return]</p>
15155 <p class=examplefilesmallCxSpMiddle>[return]</p>
15157 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15159 <p class=examplefilesmallCxSpMiddle>Which will generate:</p>
15161 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15163 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_212_252<span
15164 style="mso-spacerun: yes"> </span>211
15165 SKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAF<span style="mso-spacerun: yes">
15168 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_256_296<span
15169 style="mso-spacerun: yes"> </span>255
15170 SKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTW<span style="mso-spacerun: yes">
15173 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_300_340<span
15174 style="mso-spacerun: yes"> </span>299
15175 QNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADV<span style="mso-spacerun: yes">
15178 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_344_383<span
15179 style="mso-spacerun: yes"> </span>343 KFMVMVSSNGGQQHIAKQDLATGGV-QVLSSTFLDETPSL<span
15180 style="mso-spacerun: yes"> </span>382</p>
15182 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_387_427<span
15183 style="mso-spacerun: yes"> </span>386
15184 TMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAW<span style="mso-spacerun: yes">
15187 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15188 yes">
15189 </span>1<span style="mso-spacerun: yes"> </span>:<span
15190 style="mso-spacerun: yes"> </span>:<span
15191 style="mso-spacerun: yes"> </span>:<span
15192 style="mso-spacerun:
15193 yes"> </span>::<span
15194 style="mso-spacerun: yes">
15195 </span>.<span style="mso-spacerun: yes"> </span>40</p>
15197 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15199 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15201 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15203 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15205 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15206 yes"> </span>MENU: Type Letter
15207 Flag[number] and Return: ex |10</p>
15209 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15210 yes"> </span><span style="mso-spacerun:
15211 yes"> </span>|x<span style="mso-spacerun:
15212 yes"> </span>-->Set<span style="mso-spacerun:
15213 yes"> </span>the START to x</p>
15215 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15216 yes"> </span>>x<span
15217 style="mso-spacerun: yes"> </span>-->Set<span
15218 style="mso-spacerun: yes"> </span>the LEN<span
15219 style="mso-spacerun: yes"> </span>to x</p>
15221 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15222 yes"> </span>Cx<span
15223 style="mso-spacerun: yes"> </span>-->Set<span
15224 style="mso-spacerun: yes"> </span>the sCale to x</p>
15226 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15227 yes"> </span>Sname<span
15228 style="mso-spacerun: yes"> </span>-->Save<span
15229 style="mso-spacerun: yes"> </span>the<span
15230 style="mso-spacerun: yes"> </span>Alignment </p>
15232 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15233 yes"> </span>Bx<span
15234 style="mso-spacerun: yes"> </span>-->Save<span
15235 style="mso-spacerun: yes"> </span>Goes back x it </p>
15237 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15238 yes"> </span>return<span
15239 style="mso-spacerun: yes"> </span>-->Compute the<span
15240 style="mso-spacerun: yes"> </span>Alignment</p>
15242 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15243 yes"> </span>X<span
15244 style="mso-spacerun: yes">
15245 </span>-->eXit</p>
15247 <p class=examplefilesmallCxSpMiddle><o:p> </o:p></p>
15249 <p class=examplefilesmallCxSpLast>[ITERATION<span style="mso-spacerun:
15250 yes"> </span>3] [START=211] [LEN= 40] [SCALE=-100]<span
15251 style="mso-spacerun: yes"> </span>YOUR CHOICE: </p>
15255 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
15257 <p class=flagdescription>If you want to indicate the coordinates, relative to a
15258 specific sequence, type:</p>
15260 <p class=example2><span style='mso-tab-count:1'> </span>|<seq_name>:start</p>
15262 <p class=flagdescription>Type S<your name> to save the current alignment,
15263 and extract a new motif. </p>
15265 <p class=flagdescription>Type X when you are done.</p>
15267 <h2><a name="_Toc101065323"></a><a name="_Toc102494387"></a><a
15268 name="_Toc102494857"></a><a name="_Toc151732383"><span style='mso-bookmark:
15269 _Toc102494857'><span style='mso-bookmark:_Toc102494387'><span style='mso-bookmark:
15270 _Toc101065323'>Output Control</span></span></span></a></h2>
15272 <h3><a name="_Toc101065324"></a><a name="_Toc102494388"></a><a
15273 name="_Toc102494858"></a><a name="_Toc151732384"><span style='mso-bookmark:
15274 _Toc102494858'><span style='mso-bookmark:_Toc102494388'><span style='mso-bookmark:
15275 _Toc101065324'>Generic</span></span></span></a></h3>
15277 <p class=flag><a name="_Toc102494859"></a><a name="_Toc151732385"><span
15278 style='mso-bookmark:_Toc102494859'><span lang=AF>Conventions Regarding
15279 Filenames</span></span></a></p>
15281 <p class=MyNormal><span lang=AF>stdout, stderr, stdin, no, /dev/null are valid
15282 filenames. They cause the corresponding file to be output in stderr or stdout,
15283 for an input file, stdin causes the program to requests the corresponding file
15284 through pipe. No causes a suppression of the output, as does /dev/null.</span></p>
15286 <p class=flag><a name="_Toc102494860"></a><a name="_Toc151732386"><span
15287 style='mso-bookmark:_Toc102494860'><span lang=AF>Identifying the Output files
15288 automatically</span></span></a></p>
15290 <p class=MyNormal><span lang=AF>In the t_coffee output, each output appears in
15293 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
15294 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
15295 background:#E6E6E6'>
15297 <p class=examplefile>##### FILENAME <name> TYPE <Type> FORMAT
15302 <p class=flag><a name="_Toc101065325"></a><a name="_Toc102494389"></a><a
15303 name="_Toc102494861"></a><a name="_Toc151732387"><span style='mso-bookmark:
15304 _Toc102494861'><span style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:
15305 _Toc101065325'><span lang=AF>-no_warning</span></span></span></span></a><span
15306 style='mso-bookmark:_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span
15307 style='mso-bookmark:_Toc101065325'></span></span></span></p>
15309 <p class=flagusage><span style='mso-bookmark:_Toc102494861'><span
15310 style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc101065325'><span
15311 lang=FR>Usage:<span style="mso-spacerun: yes"> </span>-no_warning</span></span></span></span></p>
15313 <p class=instruction><span style='mso-bookmark:_Toc102494861'><span
15314 style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc101065325'>Default:
15315 Switched off</span></span></span></p>
15317 <p class=flagdescription><span style='mso-bookmark:_Toc102494861'><span
15318 style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc101065325'>Suppresseswarning
15319 output.<i style='mso-bidi-font-style:normal'><o:p></o:p></i></span></span></span></p>
15321 <h3><span style='mso-bookmark:_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span
15322 style='mso-bookmark:_Toc101065325'><o:p> </o:p></span></span></span></h3>
15324 <h3><span style='mso-bookmark:_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span
15325 style='mso-bookmark:_Toc101065325'><a name="_Toc151732388">Alignments</a></span></span></span></h3>
15327 <p class=flag><a name="_Toc101065326"></a><a name="_Toc102494862"></a><a
15328 name="_Toc151732389"><span style='mso-bookmark:_Toc102494862'><span
15329 style='mso-bookmark:_Toc101065326'><span lang=AF>-outfile</span></span></span></a></p>
15331 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
15332 </span>-outfile=<out_aln file,default,no></span></p>
15334 <p class=MyNormal><span lang=AF>Defau</span><!--[if supportFields]><span
15335 lang=AF><span style='mso-element:field-begin'></span> TOC \o "1-1" <span
15336 style='mso-element:field-separator'></span></span><![endif]--><span lang=AF><b
15337 style='mso-bidi-font-weight:normal'><span style='mso-no-proof:yes'>Word did not
15338 find any entries for your table of contents.</span></b></span><!--[if supportFields]><span
15339 lang=AF><span style='mso-element:field-end'></span></span><![endif]--><span
15340 lang=AF>lt:-outfile=default</span></p>
15342 <p class=flagdescription>Indicates the name of the alignment output by
15343 t_coffee. If the default is used, the alignment is named <i style='mso-bidi-font-style:
15344 normal'><your sequences>.aln<o:p></o:p></i></p>
15346 <p class=flag><a name="_Toc101065327"></a><a name="_Toc102494863"></a><a
15347 name="_Toc151732390"><span style='mso-bookmark:_Toc102494863'><span
15348 style='mso-bookmark:_Toc101065327'><span lang=AF>-output</span></span></span></a></p>
15350 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
15351 </span>-output=<format1,format2,...> </span></p>
15353 <p class=instruction>Default:-output=clustalw</p>
15355 <p class=flagdescription>Indicates the format used for outputting the -outfile.</p>
15357 <p class=flagdescription>Supported formats are:</p>
15359 <p class=flagdescription><span style='mso-tab-count:1'> </span></p>
15361 <p class=flagdescriptionid1>clustalw_aln, clustalw<span style='mso-tab-count:
15362 1'> </span>: ClustalW format.</p>
15364 <p class=flagdescriptionid1>gcg, msf_aln<span style="mso-spacerun:
15365 yes"> </span><span style='mso-tab-count:2'> </span>:
15368 <p class=flagdescriptionid1>pir_aln<span style='mso-tab-count:3'> </span>:
15371 <p class=flagdescriptionid1>fasta_aln<span style='mso-tab-count:2'> </span>:
15372 fasta alignment.</p>
15374 <p class=flagdescriptionid1>phylip<span style='mso-tab-count:3'> </span>:
15377 <p class=flagdescriptionid1>pir_seq<span style='mso-tab-count:3'> </span>:
15378 pir sequences (no gap).</p>
15380 <p class=flagdescriptionid1>fasta_seq<span style='mso-tab-count:2'> </span>:
15381 fasta sequences (no gap).</p>
15383 <p class=flagdescription><span style='mso-tab-count:2'> </span></p>
15385 <p class=flagdescription>As well as:</p>
15387 <p class=flagdescription><o:p> </o:p></p>
15389 <p class=flagdescriptionid1>score_ascii<span style='mso-tab-count:1'> </span>:
15390 causes the output of a reliability flag </p>
15392 <p class=flagdescriptionid1>score_html<span style='mso-tab-count:1'> </span>:
15393 causes the output to be a reliability plot in HTML</p>
15395 <p class=flagdescriptionid1>score_pdf<span style='mso-tab-count:1'> </span>:
15396 idem in PDF (if ps2pdf is installed on your system).</p>
15398 <p class=flagdescriptionid1>score_ps<span style='mso-tab-count:2'> </span>:
15399 idem in postscript.</p>
15401 <p class=flagdescription><o:p> </o:p></p>
15403 <p class=flagdescription>More than one format can be indicated:</p>
15405 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15406 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15407 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15408 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15410 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15411 sample_seq1.fasta -output=clustalw,gcg, score_html </p>
15415 <p class=flagdescription>A publication describing the CORE index is available
15418 <p class=MyNormal><span lang=AF><a
15419 href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US
15420 style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></a></span></p>
15422 <p class=flag><a name="_Toc101065328"></a><a name="_Toc102494864"></a><a
15423 name="_Toc151732391"><span style='mso-bookmark:_Toc102494864'><span
15424 style='mso-bookmark:_Toc101065328'><span lang=AF>-outseqweight</span></span></span></a></p>
15426 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
15427 </span>-outseqweight=<filename></span></p>
15429 <p class=instruction>Default: not used</p>
15431 <p class=flagdescription>Indicates the name of the file in which the sequences
15432 weights should be saved..</p>
15434 <p class=flag><a name="_Toc101065329"></a><a name="_Toc102494865"></a><a
15435 name="_Toc151732392"><span style='mso-bookmark:_Toc102494865'><span
15436 style='mso-bookmark:_Toc101065329'><span lang=AF>-case</span></span></span></a></p>
15438 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
15439 </span>-case=<keep,upper,lower></span></p>
15441 <p class=instruction>Default: -case=keep</p>
15443 <p class=MyNormal><span lang=AF>Instructs the program on the case to be used in
15444 the output file (Clustalw uses upper case). The default keeps the case and
15445 makes it possible to maintain a mixture of upper and lower case residues.</span></p>
15447 <p class=MyNormal><span lang=AF>If you need to change the case of your file,
15448 you can use seq_reformat:</span></p>
15450 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15451 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15452 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15453 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15455 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15456 –other_pg seq_reformat –in sample_aln1.aln –action +lower
15457 –output clustalw </p>
15461 <p class=flag><a name="_Toc101065330"></a><a name="_Toc102494866"></a><a
15462 name="_Toc151732393"><span style='mso-bookmark:_Toc102494866'><span
15463 style='mso-bookmark:_Toc101065330'><span lang=AF>-cpu</span></span></span></a></p>
15465 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
15466 </span>deprecated</span></p>
15468 <p class=flag><a name="_Toc102494867"></a><a name="_Toc151732394"><span
15469 style='mso-bookmark:_Toc102494867'><span lang=AF>-outseqweight</span></span></a></p>
15471 <p class=MyNormal><span lang=AF>Usage: -outseqweight=<name of the file
15472 containing the weights applied></span></p>
15474 <p class=MyNormal><span lang=AF>Default: -outseqweight=no</span></p>
15476 <p class=MyNormal><span lang=AF>Will cause the program to output the weights
15477 associated with every sequence in the dataset.</span></p>
15479 <p class=flag><a name="_Toc101065331"></a><a name="_Toc102494868"></a><a
15480 name="_Toc151732395"><span style='mso-bookmark:_Toc102494868'><span
15481 style='mso-bookmark:_Toc101065331'><span lang=AF>-outorder [cw]</span></span></span></a></p>
15483 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
15484 </span>-outorder=<input OR aligned OR filename> </span></p>
15486 <p class=instruction>Default:-outorder=input</p>
15488 <p class=flagdescription>Sets the order of the sequences in the output
15489 alignment: <b>-outorder=input</b> means the sequences are kept in the original
15490 order. <b>-outorder=aligned</b> means the sequences come in the order indicated
15491 by the tree. This order can be seen as a one-dimensional projection of the tree
15492 distances. <b style='mso-bidi-font-weight:normal'>–outdorder=<filename></b>Filename
15493 is a legal fasta file, whose order will be used in the final alignment.</p>
15495 <p class=flag><a name="_Toc151732396"><span lang=AF>-inorder [cw]</span></a></p>
15497 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
15498 </span>-inorder=<input OR aligned> </span></p>
15500 <p class=instruction>Default:-inorder=aligned</p>
15502 <p class=flagdescription>Multiple alignments based on dynamic programming
15503 depend slightly on the order in which the incoming sequences are provided. To
15504 prevent this effect sequences are arbitrarily sorted at the beginning of the
15505 program (-inorder=aligned). However, this affects the sequence order within the
15506 library. You can switch this off by ststing –inorder=input.</p>
15508 <p class=flag><a name="_Toc102494869"></a><a name="_Toc151732397"><span
15509 style='mso-bookmark:_Toc102494869'><span lang=AF>-seqnos</span></span></a></p>
15511 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
15512 </span>-seqnos=<on or off> </span></p>
15514 <p class=instruction>Default:-seqnos=off</p>
15516 <p class=MyNormal><span lang=AF>Causes the output alignment to contain residue
15517 numbers at the end of each line:</span></p>
15519 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
15520 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
15521 background:#E6E6E6'>
15523 <p class=examplefileCxSpFirst>T-COFFEE</p>
15525 <p class=examplefileCxSpMiddle>seq1 aaa---aaaa--------aa 9</p>
15527 <p class=examplefileCxSpMiddle>seq2 a-----aa-----------a 4</p>
15529 <p class=examplefileCxSpMiddle><o:p> </o:p></p>
15531 <p class=examplefileCxSpMiddle>seq1 a-----------------a 11</p>
15533 <p class=examplefileCxSpLast>seq2 aaaaaaaaaaaaaaaaaaa 19</p>
15537 <h3><a name="_Toc101065332"></a><a name="_Toc102494390"></a><a
15538 name="_Toc102494870"></a><a name="_Toc151732398"><span style='mso-bookmark:
15539 _Toc102494870'><span style='mso-bookmark:_Toc102494390'><span style='mso-bookmark:
15540 _Toc101065332'>Libraries</span></span></span></a></h3>
15542 <p class=MyNormal><span lang=AF>Although, it does not necessarily do so
15543 explicitly, T-Coffee always end up combining libraries. Libraries are
15544 collections of pairs of residues. Given a set of libraries, T-Coffee makes an
15545 attempt to assemble the alignment with the highest level of consistence. You
15546 can think of the alignment as a timetable. Each library pair would be a request
15547 from students or teachers, and the job of T-Coffee would be to assemble the
15548 time table that makes as many people as possible happy
\85</span></p>
15550 <p class=flag><a name="_Toc102494871"></a><a name="_Toc151732399"><span
15551 style='mso-bookmark:_Toc102494871'><span lang=AF>-out_lib</span></span></a></p>
15553 <p class=MyNormal><span lang=AF>Usage:<span style="mso-spacerun: yes">
15554 </span>-out_lib=<name of the library,default,no> </span></p>
15556 <p class=MyNormal><span lang=AF>Default:-out_lib=default</span></p>
15558 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
15560 <p class=flagdescription>Sets the name of the library output. Default implies
15561 <run_name>.tc_lib</p>
15563 <p class=flag><a name="_Toc101065333"></a><a name="_Toc102494872"></a><a
15564 name="_Toc151732400"><span style='mso-bookmark:_Toc102494872'><span
15565 style='mso-bookmark:_Toc101065333'><span lang=AF>-lib_only</span></span></span></a></p>
15567 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">
15568 </span>-lib_only</span></p>
15570 <p class=instruction>Default: unset</p>
15572 <p class=flagdescription>Causes the program to stop once the library has been
15573 computed. Must be used in conjunction with the flag <b style='mso-bidi-font-weight:
15574 normal'>–out_lib</b></p>
15576 <h3><a name="_Toc101065334"></a><a name="_Toc102494391"></a><a
15577 name="_Toc102494873"></a><a name="_Toc151732401"><span style='mso-bookmark:
15578 _Toc102494873'><span style='mso-bookmark:_Toc102494391'><span style='mso-bookmark:
15579 _Toc101065334'>Trees</span></span></span></a></h3>
15581 <p class=flag><a name="_Toc101065335"></a><a name="_Toc102494874"></a><a
15582 name="_Toc151732402"><span style='mso-bookmark:_Toc102494874'><span
15583 style='mso-bookmark:_Toc101065335'><span lang=AF>-newtree</span></span></span></a></p>
15585 <p class=flagusage><span lang=FR>Usage: -newtree=<tree file></span></p>
15587 <p class=instruction>Default: No file specified</p>
15589 <p class=flagdescription>Indicates the name of the file into which the guide
15590 tree will be written. The default will be <sequence_name>.dnd, or
15591 <run_name.dnd>. The tree is written in the parenthesis format known as
15592 newick or New Hampshire and used by Phylips (see the format section).</p>
15594 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
15595 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
15597 <p class=Warning>Do NOT confuse this guide tree with a phylogenetic tree.</p>
15601 <h2><a name="_Toc101065336"></a><a name="_Toc102494392"></a><a
15602 name="_Toc102494875"></a><a name="_Toc151732403"><span style='mso-bookmark:
15603 _Toc102494875'><span style='mso-bookmark:_Toc102494392'><span style='mso-bookmark:
15604 _Toc101065336'>Reliability Estimation</span></span></span></a></h2>
15606 <h3><a name="_Toc101065337"></a><a name="_Toc102494393"></a><a
15607 name="_Toc102494876"></a><a name="_Toc151732404"><span style='mso-bookmark:
15608 _Toc102494876'><span style='mso-bookmark:_Toc102494393'><span style='mso-bookmark:
15609 _Toc101065337'>CORE Computation</span></span></span></a></h3>
15611 <p class=MyNormal><span lang=AF>The CORE is an index that indicates the
15612 consistency between the library of piarwise alignments and the final multiple
15613 alignment. Our experiment indicate that the higher this consistency, the more
15614 reliable the alignment. A publication describing the CORE index can be found
15617 <p class=MyNormal><a name="_Toc101065338"></a><a name="_Toc102494877"><span
15618 style='mso-bookmark:_Toc101065338'></span></a><a
15619 href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span
15620 style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:_Toc101065338'><span
15621 style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></span></span><span
15622 style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:_Toc101065338'></span></span></a><span
15623 style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:_Toc101065338'></span></span></p>
15625 <p class=flag><span style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:
15626 _Toc101065338'><a name="_Toc151732405"><span lang=AF>-evaluate_mode</span></a></span></span></p>
15628 <p class=flagusage><span lang=FR>Usage:
15629 -evaluate_mode=<t_coffee_fast,t_coffee_slow,t_coffee_non_extended ></span></p>
15631 <p class=instruction>Default: -evaluate_mode=t_coffee_fast</p>
15633 <p class=flagdescription>This flag indicates the mode used to normalize the
15634 t_coffee score when computing the reliability score. </p>
15636 <p class=flagdescription><i style='mso-bidi-font-style:normal'>t_coffee_fast</i>:
15637 Normalization is made using the highest score in the MSA. This evaluation mode
15638 was validated and in our hands, pairs of residues with a score of 5 or higher
15639 have 90 % chances to be correctly aligned to one another. </p>
15641 <p class=flagdescription><i style='mso-bidi-font-style:normal'>t_coffee_slow:</i>
15642 Normalization is made using the library. This usually results in lower score
15643 and a scoring scheme more sensitive to the number of sequences in the dataset.
15644 Note that this scoring scheme is not any more slower, thanks to the
15645 implementation of a faster heuristic algorithm. </p>
15647 <p class=flagdescription><i style='mso-bidi-font-style:normal'>t_coffee_non_extended:</i>
15648 the score of each residue is the ratio between the sum of its non extended
15649 scores with the column and the sum of all its possible non extended scores.</p>
15651 <p class=flagdescription>These modes will be useful when generating colored
15652 version of the output, with the <b style='mso-bidi-font-weight:normal'>–output</b>
15655 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15656 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15657 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15658 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15660 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15661 sample_seq1.fasta –evaluate_mode t_coffee_slow –output score_ascii,
15664 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15665 sample_seq1.fasta –evaluate_mode t_coffee_fast –output score_ascii,
15668 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15669 sample_seq1.fasta –evaluate_mode t_coffee_non_extended –output
15670 score_ascii, score_html </p>
15674 <h2><a name="_Toc101065339"></a><a name="_Toc102494394"></a><a
15675 name="_Toc102494878"></a><a name="_Toc151732406"><span style='mso-bookmark:
15676 _Toc102494878'><span style='mso-bookmark:_Toc102494394'><span style='mso-bookmark:
15677 _Toc101065339'>Generic Output</span></span></span></a></h2>
15679 <p class=flag><a name="_Toc102494879"></a><a name="_Toc151732407"><span
15680 style='mso-bookmark:_Toc102494879'><span lang=AF>-run_name</span></span></a></p>
15682 <p class=flagusage><span lang=FR>Usage: -run_name=<your run name></span></p>
15684 <p class=instruction>Default: no default set</p>
15686 <p class=MyNormal><span lang=AF>This flag causes the prefix <your
15687 sequences> to be replaced by <your run name> when renaming the default
15688 output files.</span></p>
15690 <p class=flag><a name="_Toc101065340"></a><a name="_Toc102494880"></a><a
15691 name="_Toc151732408"><span style='mso-bookmark:_Toc102494880'><span
15692 style='mso-bookmark:_Toc101065340'><span lang=AF>-quiet</span></span></span></a></p>
15694 <p class=flagusage><span lang=FR>Usage: -quiet=<stderr,stdout,file name OR
15695 nothing>.</span></p>
15697 <p class=instruction>Default:-quiet=stderr</p>
15699 <p class=flagdescription>Redirects the standard output to either a file. <b>-quiet</b>
15700 on its own redirect the output to /dev/null.</p>
15702 <p class=flag><a name="_Toc102494881"></a><a name="_Toc151732409"><span
15703 style='mso-bookmark:_Toc102494881'><span lang=AF>-align [CW]</span></span></a></p>
15705 <p class=MyNormal><span lang=AF>This flag indicates that the program must
15706 produce the alignment. It is here for compatibility with ClustalW.</span></p>
15708 <h2><a name="_Toc151732410">APDB, iRMSD and tRMSD Parameters</a></h2>
15710 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
15712 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
15713 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
15715 <p class=Warning>Warning: These flags will only work within the APDB package
15716 that can be invoked via the –other_pg parameter of T-Coffee:</p>
15718 <p class=Warning><span style='mso-tab-count:2'> </span><span
15719 style="mso-spacerun: yes"> </span>t_coffee –other_pg apdb –aln
15720 <your aln></p>
15722 <p class=Warning><o:p> </o:p></p>
15726 <p class=flag><a name="_Toc151732411"><span lang=AF>-quiet [Same as T-Coffee]</span></a></p>
15728 <p class=flag><a name="_Toc151732412"><span lang=AF>-run_name [Same as
15729 T-Coffee]</span></a></p>
15731 <p class=flag><a name="_Toc151732413"><span lang=AF>-aln</span></a></p>
15733 <p class=flagusage><span lang=FR>Usage: -aln=<file_name>.</span></p>
15735 <p class=instruction>Default:none</p>
15737 <p class=flagdescription>Indicates the name of the file containing the
15738 sequences that need to be evaluated. The sequences whose structure is meant to
15739 be used must be named according to their PDB identifier. </p>
15741 <p class=flagdescription>The format can be FASTA, CLUSTAL or any of the formats
15742 supported by T-Coffee. APDB only evaluates residues in capital and ignores
15743 those in lower case. If your sequences are in lower case, you can upper case
15744 them using seq_reformat:</p>
15746 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15747 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15748 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15749 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15751 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15752 –other_pg seq_reformat –in 3d_sample4.aln –action +upper
15753 –output clustalw > 3d_sample4.cw_aln</p>
15757 <p class=flagdescription>The alignment can then be evaluated using the defaultr
15760 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15761 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15762 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15763 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15765 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15766 –other_pg apdb –aln 3d_sample4.aln</p>
15770 <p class=flagdescription>The alignment can contain as many structures as you
15773 <p class=flag><a name="_Toc151732414"><span lang=AF>-n_excluded_nb</span></a></p>
15775 <p class=flagusage><span lang=FR>Usage: -n_excluded_nb=<integer>.</span></p>
15777 <p class=instruction>Default:1</p>
15779 <p class=flagdescription>When evaluating the local score of a pair of aligned
15780 residues, the residues immediately next to that column should not contribute to
15781 the measure. By default the first to the left and first to the right are
15784 <p class=flag><a name="_Toc151732415"><span lang=AF>-maximum_distance</span></a></p>
15786 <p class=flagusage><span lang=FR>Usage: -maximum_distance=<float>.</span></p>
15788 <p class=instruction>Default:10</p>
15790 <p class=flagdescription>Size of the neighborhood considered around every
15791 residue. If .-local_mode is set to sphere, -maximum_distance is the radius of a
15792 sphere centered around each residue. If –local_mode is set to window,
15793 then –maximum_distance is the size of the half window (i.e. window_size=-maximum_distance*2+1).</p>
15795 <p class=flag><a name="_Toc151732416"><span lang=AF>-similarity_threshold</span></a></p>
15797 <p class=flagusage><span lang=FR>Usage: -similarity_threshold=<integer>.</span></p>
15799 <p class=instruction>Default:70</p>
15801 <p class=flagdescription>Fraction of the neighborhood that must be supportive
15802 for a pair of residue to be considered correct in APDB. The neighborhood is a
15803 sphere defined by –maximum_distance, and the support is defined by
15804 –md_threshold.</p>
15806 <p class=flag><a name="_Toc151732417"><span lang=AF>-local_mode</span></a></p>
15808 <p class=flagusage><span lang=FR>Usage: -local_mode=<sphere,window>.</span></p>
15810 <p class=instruction>Default:sphere</p>
15812 <p class=flagdescription>Defines the shape of a neighborhood, either as a
15813 sphere or as a window.</p>
15815 <p class=flag><a name="_Toc151732418"><span lang=AF>-filter</span></a></p>
15817 <p class=flagusage><span lang=FR>Usage: -filter=<0.00-1.00>.</span></p>
15819 <p class=instruction>Default:1.00</p>
15821 <p class=flagdescription>Defines the centiles that should be kept when making
15822 the local measure. Foir instance, -filter=0.90 means that the the 10 last
15823 centiles will be removed from the evaluation. The filtration is carried out on
15824 the iRMSD values.</p>
15826 <p class=flag><a name="_Toc151732419"><span lang=AF>-print_rapdb [Unsupported]</span></a></p>
15828 <p class=flagusage><span lang=FR>Usage: -print_rapdb (FLAG)</span></p>
15830 <p class=instruction>Default:off</p>
15832 <p class=flagdescription>This causes the prints out of the exact neighborhood
15833 of every considered pair of residues.</p>
15835 <p class=flag><a name="_Toc151732420"><span lang=AF>-outfile [Same as T-Coffee]</span></a></p>
15837 <p class=MyNormal><span lang=AF>This flag is meant to control the output name
15838 of the colored APDB output. This file will either display the local APDB score
15839 or the local iRMD, depending on the value of –color_mode. The default
15840 format is defined by –ouptut and is score_html.</span></p>
15842 <p class=flag><a name="_Toc151732421"><span lang=AF>-color_mode</span></a></p>
15844 <p class=flagusage><span lang=FR>Usage: -color_mode=<apdb, irmsd></span></p>
15846 <p class=instruction>Default:apdb</p>
15848 <p class=MyNormal><span lang=AF>This flag is meant to control the colored APDB
15849 output (local score). This file will either display the local APDB score or the
15850 local iRMD.</span></p>
15852 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
15853 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
15856 <p class=ChapterTitle>Building a Server</p>
15860 <p class=MyNormal><span lang=AF>We maintain a T-Coffee server
15861 (www.tcoffee.org). We will be pleased to provide anyone who wants to set up a
15862 similar service with the sources</span></p>
15864 <h3><a name="_Toc102494396"></a><a name="_Toc102494884"></a><a
15865 name="_Toc151732422"><span style='mso-bookmark:_Toc102494884'><span
15866 style='mso-bookmark:_Toc102494396'>Environment Variables</span></span></a><span
15867 style='mso-bookmark:_Toc102494884'><span style='mso-bookmark:_Toc102494396'></span></span></h3>
15869 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15870 style='mso-bookmark:_Toc102494396'><span lang=AF>T-Coffee stores a lots of
15871 information in locations that may be unsuitable when running a server. </span></span></span></p>
15873 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15874 style='mso-bookmark:_Toc102494396'><span lang=AF>By default, T-Coffee will
15875 generate and rely on the follwing directory structure:</span></span></span></p>
15877 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15878 style='mso-bookmark:_Toc102494396'>/home/youraccount/<span style='mso-tab-count:
15879 2'> </span>#HOME_4_TCOFFEE</span></span></p>
15881 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15882 style='mso-bookmark:_Toc102494396'>HOME_4_TCOFFEE/.t_coffee/ <span
15883 style='mso-tab-count:1'> </span>#DIR_4_TCOFFEE</span></span></p>
15885 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15886 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/cache<span style='mso-tab-count:
15887 2'> </span>#CACHE_4_TCOFFEE</span></span></p>
15889 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15890 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/tmp<span style='mso-tab-count:
15891 2'> </span>#TMP_4_TCOFFEE</span></span></p>
15893 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15894 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/methods<span style='mso-tab-count:
15895 2'> </span>#METHOS_4_TCOFFEE</span></span></p>
15897 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15898 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/mcoffee<span style='mso-tab-count:
15899 2'> </span>#MCOFFEE_4_TCOFFEE</span></span></p>
15901 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15902 style='mso-bookmark:_Toc102494396'><span lang=AF><o:p> </o:p></span></span></span></p>
15904 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15905 style='mso-bookmark:_Toc102494396'><span lang=AF>By default, all these
15906 directories are automatically created, following the dependencies suggested
15907 here. </span></span></span></p>
15909 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15910 style='mso-bookmark:_Toc102494396'><span lang=AF>The first step is the
15911 determination of the HOME. By default the program tries to use HOME_4_TCOFFEE,
15912 then the HOME variable and TMP or TEMP if HOME is not set on your system or
15913 your account. It is your responsibility to make sure that one of these variables
15914 is set to some valid location where the T-Coffee process is allowed to read and
15915 write.</span></span></span></p>
15917 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15918 style='mso-bookmark:_Toc102494396'><span lang=AF>If no valid location can be
15919 found for HOME_4_TCOFFEE, the program exits. If you are running T-Coffee on a
15920 server, we recommend to hard set the following locations, where your scratch is
15921 a valid location. </span></span></span></p>
15923 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15924 style='mso-bookmark:_Toc102494396'><span lang=AF><o:p> </o:p></span></span></span></p>
15926 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15927 style='mso-bookmark:_Toc102494396'>HOME_4_TCOFFEE=
\94your scratch
\94</span></span></p>
15929 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15930 style='mso-bookmark:_Toc102494396'>TMP_4_TCOFFEE=
\94your scratch
\94</span></span></p>
15932 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15933 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE=
\94your scratch
\94</span></span></p>
15935 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15936 style='mso-bookmark:_Toc102494396'>CACHE_4_TCOFFEE=
\94your scratch
\94</span></span></p>
15938 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15939 style='mso-bookmark:_Toc102494396'>NO_ERROR_REPORT_4_TCOFFEE=1</span></span></p>
15941 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15942 style='mso-bookmark:_Toc102494396'><span lang=AF>Note that<span
15943 style="mso-spacerun: yes"> </span>it is a good idea to have a cron job
15944 that cleans up this scratch area, once in a while. </span></span></span></p>
15946 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15947 style='mso-bookmark:_Toc102494396'><span lang=AF><o:p> </o:p></span></span></span></p>
15949 <h3><span style='mso-bookmark:_Toc102494884'><span style='mso-bookmark:_Toc102494396'><a
15950 name="_Toc151732423">Output of the .dnd file.</a></span></span></h3>
15952 <p class=MyNormal><span lang=AF>A common source of error when running a server:
15953 T-Coffee MUST output the .dnd file because it re-reads it to carry out the
15954 progressive alignment. By default T-Coffee outputs this file in the directory where
15955 the process is running. If the T-Coffee process does not have permission to
15956 write in that directory, the computation will abort...</span></p>
15958 <p class=MyNormal><span lang=AF>To avoid this, simply specify the name of the
15959 output tree: </span></p>
15961 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-newtree=<writable
15962 file (usually in /tmp)></span></p>
15964 <p class=MyNormal><span lang=AF>Chose the name so that two processes may not
15965 over-write each other dnd file. </span></p>
15967 <h3><a name="_Toc102494397"></a><a name="_Toc102494885"></a><a
15968 name="_Toc151732424"><span style='mso-bookmark:_Toc102494885'><span
15969 style='mso-bookmark:_Toc102494397'>Permissions</span></span></a></h3>
15971 <p class=MyNormal><span lang=AF>The t_coffee process MUST be allowed to write
15972 in some scratch area, even when it is ran by Mr nobody... Make sure the /tmp/
15973 partition is not protected.</span></p>
15975 <h3><a name="_Toc102494398"></a><a name="_Toc102494886"></a><a
15976 name="_Toc151732425"><span style='mso-bookmark:_Toc102494886'><span
15977 style='mso-bookmark:_Toc102494398'>Other Programs</span></span></a></h3>
15979 <p class=MyNormal><span lang=AF>T-Coffee may call various programs while it
15980 runs (lalign2list by defaults). Make sure your process knows where to find
15981 these executables.</span></p>
15983 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
15984 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
15987 <p class=ChapterTitle><a name="_Toc101065353"></a><a name="_Toc102494887"><span
15988 style='mso-bookmark:_Toc101065353'>F</span></a>ormats</p>
15992 <h2><a name="_Toc101065354"></a><a name="_Toc102494399"></a><a
15993 name="_Toc102494888"></a><a name="_Toc151732426"><span style='mso-bookmark:
15994 _Toc102494888'><span style='mso-bookmark:_Toc102494399'><span style='mso-bookmark:
15995 _Toc101065354'>Parameter files</span></span></span></a></h2>
15997 <p class=MyNormal><span lang=AF>Parameter files used with -parameters,
15998 -t_coffee_defaults, -dali_defaults... Must contain a valid parameter string
15999 where line breaks are allowed. These files cannot contain any comment, the
16000 recommended format is one parameter per line:</span></p>
16002 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16003 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16004 background:#E6E6E6'>
16006 <p class=examplefileCxSpFirst><span style='mso-tab-count:1'> </span><parameter
16007 name>=<value1>,<value2>....</p>
16009 <p class=examplefileCxSpLast><span style='mso-tab-count:1'> </span><parameter
16014 <h2><a name="_Toc101065355"></a><a name="_Toc102494400"></a><a
16015 name="_Toc102494889"></a><a name="_Toc151732427"><span style='mso-bookmark:
16016 _Toc102494889'><span style='mso-bookmark:_Toc102494400'><span style='mso-bookmark:
16017 _Toc101065355'>Sequence Name Handling</span></span></span></a></h2>
16019 <p class=MyNormal><span lang=AF>Sequence name handling is meant to be fully
16020 consistent with ClustalW (Version 1.75). This implies that in some cases the
16021 names of your sequences may be edited when coming out of the program. Five
16022 rules apply:</span></p>
16024 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
16026 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16027 mso-border-alt:solid windowtext .5pt;padding:1.0pt 1.0pt 1.0pt 1.0pt'>
16029 <p class=Noteboxtitle style='border:none;mso-border-alt:solid windowtext .5pt;
16030 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Naming Your Sequences the
16033 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16034 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>1-No Space</p>
16036 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16037 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Names that do contain
16038 spaces, for instance:</p>
16040 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16041 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span style='mso-tab-count:
16042 1'> </span>>seq1
16045 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16046 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>will be turned into</p>
16048 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16049 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span style='mso-tab-count:
16050 1'> </span>>seq1</p>
16052 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16053 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>It is your responsibility
16054 to make sure that the names you provide are not ambiguous after such an
16055 editing. This editing is consistent with Clustalw (Version 1.75)</p>
16057 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16058 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><o:p> </o:p></p>
16060 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16061 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>2-No Strange Character</p>
16063 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16064 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Some non alphabetical characters
16065 are replaced with underscores. These are: ';:()'</p>
16067 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16068 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Other characters are legal
16069 and will be kept unchanged. This editing is meant to keep in line with Clustalw
16070 (Version 1.75).</p>
16072 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16073 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><o:p> </o:p></p>
16075 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16076 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>3-> is NEVER legal
16077 (except as a header token in a FASTA file)</p>
16079 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16080 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><o:p> </o:p></p>
16082 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16083 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>4-Name length must be
16084 below 100 characters, although 15 is recommended for compatibility with other
16087 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16088 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>5-Duplicated sequences
16089 will be renamed (i.e. sequences with the same name in the same dataset) are
16090 allowed but will be renamed according to their original order. When sequences
16091 come from multiple sources via the –in flag, consistency of the renaming
16092 is not guaranteed. You should avoid duplicated sequences as they will cause
16093 your input to differ from your output thus making it difficult to track data.</p>
16097 <h2><a name="_Toc101065356"></a><a name="_Toc102494401"></a><a
16098 name="_Toc102494890"></a><a name="_Toc151732428"><span style='mso-bookmark:
16099 _Toc102494890'><span style='mso-bookmark:_Toc102494401'><span style='mso-bookmark:
16100 _Toc101065356'>Automatic Format Recognition</span></span></span></a></h2>
16102 <p class=MyNormal><span lang=AF>Most common formats are automatically
16103 recognized by t_coffee. See -in and the next section for more details. If your
16104 format is not recognized, use readseq or clustalw to switch to another format.
16105 We recommend Fasta.</span></p>
16107 <h2><a name="_Toc101065357"></a><a name="_Toc102494402"></a><a
16108 name="_Toc102494891"></a><a name="_Toc151732429"><span style='mso-bookmark:
16109 _Toc102494891'><span style='mso-bookmark:_Toc102494402'><span style='mso-bookmark:
16110 _Toc101065357'>Structures</span></span></span></a></h2>
16112 <p class=MyNormal><span lang=AF>PDB format is recognized by T-Coffee. T-Coffee
16113 uses extract_from_pdb (cf –other_pg flag). extract_from_pdb is a small
16114 embeded module that can be used on its own to extract information from pdb
16117 <h2><a name="_Toc151732430">RNA Structures</a></h2>
16119 <p class=MyNormal><span lang=AF>RNA structures can either be coded as T-Coffee
16120 libraries, with each line indicating two paired residues, or as alifold output.
16121 The selex format is also partly supported (see the seq_reformat tutorial on RNA
16122 sequences handling).</span></p>
16124 <h2><a name="_Toc101065358"></a><a name="_Toc102494403"></a><a
16125 name="_Toc102494892"></a><a name="_Toc151732431"><span style='mso-bookmark:
16126 _Toc102494892'><span style='mso-bookmark:_Toc102494403'><span style='mso-bookmark:
16127 _Toc101065358'>Sequences</span></span></span></a></h2>
16129 <p class=MyNormal><span lang=AF>Sequences can come in the following formats:
16130 fasta, pir, swiss-prot, clustal aln, msf aln and t_coffee aln. These formats
16131 are the one automatically recognized. Please replace the '*' sign sometimes
16132 used for stop codons with an X.</span></p>
16134 <h2><a name="_Toc101065359"></a><a name="_Toc102494404"></a><a
16135 name="_Toc102494893"></a><a name="_Toc151732432"><span style='mso-bookmark:
16136 _Toc102494893'><span style='mso-bookmark:_Toc102494404'><span style='mso-bookmark:
16137 _Toc101065359'>Alignments</span></span></span></a></h2>
16139 <p class=MyNormal><span lang=AF>Alignments can come in the following formats:
16140 msf, ClustalW, Fasta, Pir and t_coffee. The t_coffee format is very similar to
16141 the ClustalW format, but slightly more flexible. Any interleaved format with
16142 sequence name on each line will be correctly parsed:</span></p>
16144 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16145 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16146 background:#E6E6E6'>
16148 <p class=examplefileCxSpFirst><empy line> <span style='mso-tab-count:
16149 1'> </span>[Facultative]n</p>
16151 <p class=examplefileCxSpMiddle><line of text> <span style='mso-tab-count:
16152 1'> </span>[Required]</p>
16154 <p class=examplefileCxSpMiddle><line of text><span style='mso-tab-count:
16155 3'> </span>[Facultative]n</p>
16157 <p class=examplefileCxSpMiddle><empty line><span style='mso-tab-count:
16158 3'> </span>[Required]</p>
16160 <p class=examplefileCxSpMiddle><empty line><span style='mso-tab-count:
16161 3'> </span>[Facultative]n</p>
16163 <p class=examplefileCxSpMiddle><seq1 name><space><seq1></p>
16165 <p class=examplefileCxSpMiddle><seq2 name><space><seq2></p>
16167 <p class=examplefileCxSpMiddle><seq3 name><space><seq3></p>
16169 <p class=examplefileCxSpMiddle><empty line><span style='mso-tab-count:
16170 3'> </span>[Required]</p>
16172 <p class=examplefileCxSpMiddle><empty line><span style='mso-tab-count:
16173 3'> </span>[Facultative]n</p>
16175 <p class=examplefileCxSpMiddle><seq1 name><space><seq1></p>
16177 <p class=examplefileCxSpMiddle><seq2 name><space><seq2></p>
16179 <p class=examplefileCxSpMiddle><seq3 name><space><seq3></p>
16181 <p class=examplefileCxSpMiddle><empty line><span style='mso-tab-count:
16182 3'> </span>[Required]</p>
16184 <p class=examplefileCxSpLast><empty line><span style='mso-tab-count:3'> </span>[Facultative]n</p>
16188 <p class=MyNormal><span lang=AF>An empty line is a line that does NOT contain
16189 amino-acid. A line that contains the ClustalW annotation (.:*) is empty.</span></p>
16191 <p class=MyNormal><span lang=AF>Spaces are forbidden in the name. When the
16192 alignment is being read, non character signs are ignored in the sequence field
16193 (such as numbers, annotation
\85).</span></p>
16195 <p class=Note><span style='mso-ansi-language:EN-US'>Note: a different number of
16196 lines in the different blocks will cause the program to crash or hang.<o:p></o:p></span></p>
16198 <h2><a name="_Toc101065360"></a><a name="_Toc102494405"></a><a
16199 name="_Toc102494894"></a><a name="_Toc151732433"><span style='mso-bookmark:
16200 _Toc102494894'><span style='mso-bookmark:_Toc102494405'><span style='mso-bookmark:
16201 _Toc101065360'>Libraries</span></span></span></a></h2>
16203 <h3><a name="_Toc102494406"></a><a name="_Toc102494895"></a><a
16204 name="_Toc151732434"><span style='mso-bookmark:_Toc102494895'><span
16205 style='mso-bookmark:_Toc102494406'>T-COFFEE_LIB_FORMAT_01</span></span></a></h3>
16207 <p class=MyNormal><span lang=AF>This is currently the only supported format.</span></p>
16209 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16210 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16211 background:#E6E6E6'>
16213 <p class=examplefileCxSpFirst>!<space> TC_LIB_FORMAT_01</p>
16215 <p class=examplefileCxSpMiddle><nseq></p>
16217 <p class=examplefileCxSpMiddle><seq1 name> <seq1 length>
16220 <p class=examplefileCxSpMiddle><seq2 name> <seq2 length>
16223 <p class=examplefileCxSpMiddle><seq3 name> <seq3 length>
16226 <p class=examplefileCxSpMiddle>!Comment</p>
16228 <p class=examplefileCxSpMiddle>(!Comment)n</p>
16230 <p class=examplefileCxSpMiddle>#Si1 Si2</p>
16232 <p class=examplefileCxSpMiddle>Ri1 Ri2 V1 (V2, V3)</p>
16234 <p class=examplefileCxSpMiddle>#1 2</p>
16236 <p class=examplefileCxSpMiddle>12 13 99 (12/0 vs 13/1, weight 99)</p>
16238 <p class=examplefileCxSpMiddle>12 14 70</p>
16240 <p class=examplefileCxSpMiddle>15 16 56</p>
16242 <p class=examplefileCxSpMiddle>#1 3</p>
16244 <p class=examplefileCxSpMiddle>12 13 99 </p>
16246 <p class=examplefileCxSpMiddle>12 14 70</p>
16248 <p class=examplefileCxSpMiddle>15 16 56</p>
16250 <p class=examplefileCxSpLast>!<space>SEQ_1_TO_N </p>
16254 <p class=MyNormal><span lang=AF>Si1: index of Sequence 1</span></p>
16256 <p class=MyNormal><span lang=AF>Ri1: index of residue 1 in seq1</span></p>
16258 <p class=MyNormal><span lang=AF>V1: Integer Value: Weight</span></p>
16260 <p class=MyNormal><span lang=AF>V2, V3: optional values</span></p>
16262 <p class=Note><span style='mso-ansi-language:EN-US'>Note 1: There is a space
16263 between the ! And SEQ_1_TO_N<o:p></o:p></span></p>
16265 <p class=Note><span style='mso-ansi-language:EN-US'>Note 2: The last line (!
16266 SEQ_1_TO_N) indicates that:<o:p></o:p></span></p>
16268 <p class=MyNormal><span lang=AF>Sequences and residues are numbered from 1 to
16269 N, unless the token SEQ_1_TO_N is omitted, in which case the sequences are
16270 numbered from 0 to N-1, and residues are from 1 to N.</span></p>
16272 <p class=MyNormal><span lang=AF>Residues do not need to be sorted, and neither
16273 do the sequences. The same pair can appear several times in the library. For
16274 instance, the following file would be legal:</span></p>
16276 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16277 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16278 background:#E6E6E6'>
16280 <p class=examplefileCxSpFirst>#1 2</p>
16282 <p class=examplefileCxSpMiddle>12 13 99</p>
16284 <p class=examplefileCxSpMiddle>#1 2</p>
16286 <p class=examplefileCxSpMiddle>15 16 99 </p>
16288 <p class=examplefileCxSpMiddle>#1 1</p>
16290 <p class=examplefileCxSpLast>12 14 70</p>
16294 <p class=MyNormal><a name="_Toc102494407"></a><a name="_Toc102494896"><span
16295 style='mso-bookmark:_Toc102494407'><span lang=AF>It is also poosible to declare
16296 ranges of resdues rather than single pairs. For instance, the following:</span></span></a></p>
16298 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16299 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16300 background:#E6E6E6'>
16302 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494896'><span
16303 style='mso-bookmark:_Toc102494407'>#0 1</span></span></p>
16305 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16306 style='mso-bookmark:_Toc102494407'>+BLOCK+<span style="mso-spacerun:
16307 yes"> </span>10 12 14 99</span></span></p>
16309 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16310 style='mso-bookmark:_Toc102494407'>+BLOCK+<span style="mso-spacerun:
16311 yes"> </span>15 30 40 99</span></span></p>
16313 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16314 style='mso-bookmark:_Toc102494407'>#0 2</span></span></p>
16316 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16317 style='mso-bookmark:_Toc102494407'>15 16 99 </span></span></p>
16319 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16320 style='mso-bookmark:_Toc102494407'>#0 1</span></span></p>
16322 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494896'><span
16323 style='mso-bookmark:_Toc102494407'>12 14 70</span></span></p>
16327 <p class=MyNormal><span style='mso-bookmark:_Toc102494896'><span
16328 style='mso-bookmark:_Toc102494407'><span lang=AF>The first statement BLOCK
16329 declares a BLOCK of length 10, that starts on position 12 of sequence 1 and
16330 position 14 of sequence 2 and where each pair of residues within the block has
16331 a score of 99. The second BLOCK starts on residue 30 of 1, residue 40 of 2 and
16332 extends for 15 residues.</span></span></span></p>
16334 <p class=MyNormal><span style='mso-bookmark:_Toc102494896'><span
16335 style='mso-bookmark:_Toc102494407'><span lang=AF>Blocks can overalp and be
16336 incompatible with one another, just like single constraints.</span></span></span></p>
16338 <p class=MyNormal><span style='mso-bookmark:_Toc102494896'><span
16339 style='mso-bookmark:_Toc102494407'><span lang=AF><span style="mso-spacerun:
16340 yes"> </span></span></span></span></p>
16342 <h3><span style='mso-bookmark:_Toc102494896'><span style='mso-bookmark:_Toc102494407'><a
16343 name="_Toc151732435">T-COFFEE_LIB_FORMAT_02</a></span></span></h3>
16345 <p class=MyNormal><span lang=AF>A simpler format is being developed, however it
16346 is not yet fully supported and is only mentioned here for development purpose.</span></p>
16348 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16349 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16350 background:#E6E6E6'>
16352 <p class=examplefileCxSpFirst>! TC_LIB_FORMAT_02</p>
16354 <p class=examplefileCxSpMiddle>#S1 SEQ1 [OPTIONAL]</p>
16356 <p class=examplefileCxSpMiddle>#S2 SEQ2 [OPTIONAL]</p>
16358 <p class=examplefileCxSpMiddle>...</p>
16360 <p class=examplefileCxSpMiddle>!comment [OPTIONAL]</p>
16362 <p class=examplefileCxSpMiddle>S1 R1 Ri1 S2 R2 Ri2 V1 (V2 V3)</p>
16364 <p class=examplefileCxSpMiddle>=> N R1 Ri1 S2 R2 Ri2 V1 (V2 V3)</p>
16366 <p class=examplefileCxSpLast>...</p>
16370 <p class=MyNormal><span lang=AF>S1, S2: name of sequence 1 and 2</span></p>
16372 <p class=MyNormal><span lang=AF>SEQ1: sequence of S1</span></p>
16374 <p class=MyNormal><span lang=AF>Ri1, Ri2: index of the residues in their
16375 respective sequence</span></p>
16377 <p class=MyNormal><span lang=AF>R1, R2: Residue type</span></p>
16379 <p class=MyNormal><span lang=AF>V1, V2, V3: integer Values (V2 and V3 are
16380 optional)</span></p>
16382 <p class=MyNormal><span lang=AF>Value1, Value 2 and Value3 are optional.</span></p>
16384 <h2><a name="_Toc101065361"></a><a name="_Toc102494408"></a><a
16385 name="_Toc102494897"></a><a name="_Toc151732436"><span style='mso-bookmark:
16386 _Toc102494897'><span style='mso-bookmark:_Toc102494408'><span style='mso-bookmark:
16387 _Toc101065361'>Library List</span></span></span></a><span style='mso-bookmark:
16388 _Toc101065361'></span></h2>
16390 <p class=MyNormal><span style='mso-bookmark:_Toc101065361'><span lang=AF>These
16391 are lists of pairs of sequences that must be used to compute a library. The
16392 format is:</span></span></p>
16394 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16395 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16396 background:#E6E6E6'>
16398 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065361'><nseq>
16399 <S1> <S2></span></p>
16401 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'>2 hamg2
16404 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'>3 hamgw
16405 hemog singa</span></p>
16407 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065361'>...</span></p>
16411 <h2><span style='mso-bookmark:_Toc101065361'><a name="_Toc102494409"></a><a
16412 name="_Toc102494898"></a><a name="_Toc151732437"><span style='mso-bookmark:
16413 _Toc102494898'><span style='mso-bookmark:_Toc102494409'>Substitution matrices.</span></span></a></span></h2>
16415 <p class=MyNormal><span lang=AF>If the required substitution matrix is not
16416 available, write your own in a file using the following format:</span></p>
16418 <h3><a name="_Toc101065362"></a><a name="_Toc102494410"></a><a
16419 name="_Toc102494899"></a><a name="_Toc151732438"><span style='mso-bookmark:
16420 _Toc102494899'><span style='mso-bookmark:_Toc102494410'><span style='mso-bookmark:
16421 _Toc101065362'>ClustalW Style</span> [Deprecated]</span></span></a></h3>
16423 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16424 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16425 background:#E6E6E6'>
16427 <p class=examplefileCxSpFirst># CLUSTALW_MATRIX FORMAT</p>
16429 <p class=examplefileCxSpMiddle>$</p>
16431 <p class=examplefileCxSpMiddle>v1</p>
16433 <p class=examplefileCxSpMiddle>v2 v3</p>
16435 <p class=examplefileCxSpMiddle>v4 v5 v6</p>
16437 <p class=examplefileCxSpMiddle>...</p>
16439 <p class=examplefileCxSpLast>$</p>
16443 <p class=MyNormal><span lang=AF>v1, v2... are integers, possibly negatives.</span></p>
16445 <p class=MyNormal><span lang=AF>The order of the amino acids is:
16446 ABCDEFGHIKLMNQRSTVWXYZ, which means that v1 is the substitution value for A vs
16447 A, v2 for A vs B, v3 for B vs B, v4 for A vs C and so on.</span></p>
16449 <h3><a name="_Toc101065363"></a><a name="_Toc102494411"></a><a
16450 name="_Toc102494900"></a><a name="_Toc151732439"><span style='mso-bookmark:
16451 _Toc102494900'><span style='mso-bookmark:_Toc102494411'><span style='mso-bookmark:
16452 _Toc101065363'>BLAST Format [Recommended]</span></span></span></a></h3>
16454 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16455 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16456 background:#E6E6E6'>
16458 <p class=examplefileCxSpFirst># BLAST_MATRIX FORMAT</p>
16460 <p class=examplefileCxSpMiddle># ALPHABET=AGCT</p>
16462 <p class=examplefileCxSpMiddle><span style="mso-spacerun: yes"> </span>A G
16465 <p class=examplefileCxSpMiddle>A 0 1 2 3</p>
16467 <p class=examplefileCxSpMiddle>G 0 2 3 4</p>
16469 <p class=examplefileCxSpMiddle>C 1 1 2 3</p>
16471 <p class=examplefileCxSpLast>...</p>
16475 <p class=MyNormal><span lang=AF>The alphabet can be freely defined</span></p>
16477 <h2><a name="_Toc101065364"></a><a name="_Toc102494412"></a><a
16478 name="_Toc102494901"></a><a name="_Toc151732440"><span style='mso-bookmark:
16479 _Toc102494901'><span style='mso-bookmark:_Toc102494412'><span style='mso-bookmark:
16480 _Toc101065364'>Sequences Weights</span></span></span></a></h2>
16482 <p class=MyNormal><span lang=AF>Create your own weight file, using the
16483 -seq_weight flag:</span></p>
16485 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16486 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16487 background:#E6E6E6'>
16489 <p class=examplefileCxSpFirst># SINGLE_SEQ_WEIGHT_FORMAT_01</p>
16491 <p class=examplefileCxSpMiddle>seq_name1 v1</p>
16493 <p class=examplefileCxSpMiddle>seq_name2 v2</p>
16495 <p class=examplefileCxSpLast>...</p>
16499 <p class=MyNormal><span lang=AF>No duplicate allowed. Sequences not included in
16500 the set of sequences provided to t_coffee will be ignored. Order is free. V1 is
16501 a float. Un-weighted sequences will see their weight set to 1.</span></p>
16503 <span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:
16504 "Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;
16505 mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:always'>
16508 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
16509 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
16512 <p class=ChapterTitle>Known Problems</p>
16516 <p class=MyNormal><span lang=AF>1-Sensitivity to sequence order: It is
16517 difficult to implement a MSA algorithm totally insensitive to the order of
16518 input of the sequences. In t_coffee, robustness is increased by sorting the
16519 sequences alphabetically before aligning them. Beware that this can result in
16520 confusing output where sequences with similar name are unexpectedly close to
16521 one another in the final alignment.</span></p>
16523 <p class=MyNormal><span lang=AF>2-Nucleotides sequences with long stretches of
16524 Ns will cause problems to lalign, especially when using Mocca. To avoid any
16525 problem, filter out these nucleotides before running mocca.</span></p>
16527 <p class=MyNormal><span lang=AF>3-Stop codons are sometimes coded with '*' in
16528 protein sequences. This will cause the program to crash or hang. Please replace
16529 the '*' signs with an X.</span></p>
16531 <p class=MyNormal><span lang=AF>4-Results can differ from one architecture to
16532 another, due rounding differences. This is caused by the tree estimation
16533 procedcure. If you want to make sure an alignment is reproducible, you should
16534 keep the associated dendrogram.</span></p>
16536 <p class=MyNormal><span lang=AF>5-Deploying the program on a </span></p>
16538 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
16539 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
16542 <p class=ChapterTitle>Technical Notes</p>
16546 <p class=MyNormal><span lang=AF>These notes are only meant for internal
16547 development.</span></p>
16549 <h2><a name="_Toc102494413"></a><a name="_Toc102494904"></a><a
16550 name="_Toc151732441"><span style='mso-bookmark:_Toc102494904'><span
16551 style='mso-bookmark:_Toc102494413'>Development</span></span></a></h2>
16553 <p class=MyNormal><span lang=AF>The following examples are only meant for
16554 internal development, and are used to insure stability from release to release</span></p>
16556 <h4><a name="_Toc151732442"><span lang=AF>profile2list</span></a></h4>
16558 <p class=MyNormal><span lang=AF>prf1: profile containing one structure</span></p>
16560 <p class=MyNormal><span lang=AF>prf2: profile containing one structure</span></p>
16562 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
16564 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16565 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16566 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16567 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16569 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT:
16570 t_coffee<span style="mso-spacerun: yes"> </span>Rsample_profile1.aln,Rsample_profile2.aln
16571 -mode=3dcoffee -outfile=aligned_prf.aln</p>
16573 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><o:p> </o:p></p>
16577 <h3><a name="_Toc102494414"></a><a name="_Toc102494905"></a><a
16578 name="_Toc151732443"><span style='mso-bookmark:_Toc102494905'><span
16579 style='mso-bookmark:_Toc102494414'>Command Line List</span></span></a></h3>
16581 <p class=MyNormal><span lang=AF>These command lines have been checked before
16582 every release (along with the other CL in this documentation:</span></p>
16584 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
16586 <p class=MyNormal><span lang=AF>-external methods;</span></p>
16588 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16589 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16590 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16591 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16593 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
16594 style='mso-tab-count:1'> </span>PROMPT: t_coffee sample_seq1.fasta
16595 –in=Mclustalw_pair,Mclustalw_msa,Mslow_pair –outfile=clustal_text</p>
16599 <p class=MyNormal><span lang=AF>-fugue_client</span></p>
16601 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16602 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16603 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16604 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16606 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16607 –in Ssample_seq5.fasta Pstruc4.pdb Mfugue_pair</p>
16611 <p class=MyNormal><span lang=AF>-A list of command lines kindly provided by
16612 James Watson (used to crash the pg before version 3.40)</span></p>
16614 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16615 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16616 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16617 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16619 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16620 -in Sseq.fas P2PTC Mfugue_pair</p>
16622 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16623 -in S2seqs.fas Mfugue_pair -template_file SELF_P_</p>
16625 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee -mode
16626 3dcoffee -in Sseq.fas P2PTC</p>
16628 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee -mode
16629 3dcoffee -in S2seqs.fas -template_file SELF_P_</p>
16633 <p class=MyNormal><span lang=AF>-A list of command lines that crashed the
16634 program before 3.81</span></p>
16636 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16637 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16638 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16639 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16641 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16642 sample_seq6.fasta –in Mfast_pair Msap_pair Mfugue_pair
16643 –template_file template_file6.template </p>
16647 <p class=MsoBodyText><span style='mso-tab-count:1'> </span>-A
16648 command line to read
\93relaxed
\94 pdb files...</p>
16650 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16651 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16652 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16653 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16655 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16656 –in Msap_pair Ssample_seq7.fasta –template_file template_file7.template
16657 –weight 1001 –out_lib test_lib7.tc_lib –lib_only </p>
16661 <p class=MsoBodyText><span style='mso-tab-count:1'> </span>-Parsing
16662 of MARNA libraries</p>
16664 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16665 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16666 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16667 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16669 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16670 –in Lmarna.tc_lib –outfile maran.test</p>
16674 <p class=MsoBodyText><span style='mso-tab-count:1'> </span>-Parsing
16675 of long sequence lines:</p>
16677 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16678 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16679 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16680 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16682 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16683 –in Asample_aln5.aln –outfile test.aln</p>
16687 <p class=MsoBodyText><o:p> </o:p></p>
16689 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
16690 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
16693 <p class=ChapterTitle><a name="_Toc102494906">To D</a>o
\85</p>
16697 <p class=MyNormal><span lang=AF>-implement UPGMA tree computation</span></p>
16699 <p class=MyNormal><span lang=AF>-implement seq2dpa_tree</span></p>
16701 <p class=MyNormal><span lang=AF>-debug dpa</span></p>
16703 <p class=MyNormal><span lang=AF>-Reconciliate sequences and template when
16704 reading the template</span></p>
16706 <p class=MyNormal><span lang=AF>-Add the server command lines to the checking
16707 procedure</span></p>
16709 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
16711 <p class=MsoNormal><o:p> </o:p></p>
16713 <p class=MsoNormal><o:p> </o:p></p>
16715 <p class=MsoNormal><o:p> </o:p></p>
16717 <p class=MsoBodyText><o:p> </o:p></p>