source: tags/initial/GDEHELP/ARB_GDEmenus

Last change on this file was 2, checked in by oldcode, 25 years ago

Initial revision
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  • Property svn:keywords set to Author Date Id Revision
File size: 25.4 KB
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5 #      WARNING:        this file is created automatically
6 #      edit            ARB_GDEmenus.source and MENUS/xxx.menu instead
7 #      and run make in this directory
8
9 #      To get more information read GDE2.2_manual_text
10 #      I added two new argtypes:
11 #              argtype:tree    A list of trees in the database
12 #              argtype:weights A list of conservation profiles in the db
13
14
15
16lmenu:export
17item:Export Sequences only to Foreign Format (using readseq: slow) ...
18 
19itemmethod:arb_readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE
20itemhelp:readseq.help
21
22arg:FORMAT
23argtype:choice_menu
24argchoice:GenBank:genbank
25argchoice:IG/Stanford:ig
26argchoice:NBRF:nbrf
27argchoice:EMBL:embl
28argchoice:GCG:gcg
29argchoice:DNA Strider:strider
30argchoice:Fitch:fitch
31argchoice:Pearson/Fasta:pearson
32argchoice:Zuker:zuker
33argchoice:Olsen:olsen
34argchoice:Phylip:phylip
35argchoice:Plain text:raw
36argchoice:ASN.1:asn
37argchoice:PIR:pir
38argchoice:MSF:msf
39argchoice:PAUP:paup
40argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop
41
42arg:OUTPUTFILE
43argtype:text
44arglabel:Save as?
45
46in:in1
47informat:genbank
48
49
50lmenu:pretty_print
51item:Pretty Print Sequences (slow) ...
52 
53
54
55
56
57
58itemmethod:arb_readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (arb_textprint in1.pretty; /bin/rm -f in1 in1.pretty )&
59itemhelp:readseq.help
60in:in1
61informat:genbank
62 
63arg:NAMETOP
64argtype:chooser
65arglabel:Names at top  ?
66argchoice:No:
67argchoice:Yes:-nametop
68 
69arg:NAMELEFT
70argtype:chooser
71arglabel:Names at left ?
72argchoice:No:
73argchoice:Yes:-nameleft
74 
75arg:NAMERIGHT
76argtype:chooser
77arglabel:Names at right?
78argchoice:Yes:-nameright
79argchoice:No:
80 
81arg:NUMTOP
82argtype:chooser
83arglabel:Numbers at top  ?
84argchoice:Yes:-numtop
85argchoice:No:
86 
87arg:NUMBOT
88argtype:chooser
89arglabel:Numbers at tail ?
90argchoice:No:
91argchoice:Yes:-numbot
92 
93arg:NUMLEFT
94argtype:chooser
95arglabel:Numbers at left ?
96argchoice:Yes:-numleft
97argchoice:No:
98 
99arg:NUMRIGHT
100argtype:chooser
101arglabel:Numbers at right?
102argchoice:Yes:-numright
103argchoice:No:
104
105arg:MATCH
106argtype:chooser
107arglabel:Show difference to current species?
108argchoice:No:
109argchoice:Yes:-match
110 
111arg:GAPC
112argtype:chooser
113arglabel:Count gap symbols?
114argchoice:No:
115argchoice:Yes:-gap
116 
117arg:WIDTH
118argtype:slider
119arglabel:Sequence width?
120argmin:10
121argmax:200
122argvalue:100
123 
124arg:COLS
125argtype:slider
126arglabel:Column spacers?
127argmin:0
128argmax:50
129argvalue:10
130 
131
132
133lmenu:import
134item:Import Sequences in Foreign Format (using readseq: slow !!) ...
135 
136
137
138
139itemmethod:arb_readseq $INPUTFILE -a -f2 > OUTPUTFILE
140itemhelp:readseq.help
141
142arg:INPUTFILE
143argtype:text
144arglabel:Name of foreign file?
145
146out:OUTPUTFILE
147outformat:genbank
148
149 
150
151item:Test arb_jim ...
152
153
154itemmethod:arb_jim
155itemhelp:jim.help
156
157
158out:OUTPUTFILE
159outformat:genbank
160
161 
162
163
164menu:align
165arb_item:Clustalv Alignment (DNA)
166itemmethod:(tr '"%//' '>' <in1 >clus_in; ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; /bin/rm -f clus_in* in1)
167
168itemhelp:clustal_help
169
170arg:KTUP
171argtype:slider
172arglabel:K-tuple size for fast pairwise search
173argmin:1
174argmax:10
175argvalue:2
176
177arg:WIN
178argtype:slider
179arglabel:Window size
180argmin:1
181argmax:10
182argvalue:4
183
184arg:Trans
185argtype:chooser
186arglabel:Transitions weighted?
187argchoice:Yes:/TRANSIT
188argchoice:No:
189
190arg:FIXED
191argtype:slider
192arglabel:Fixed gap penalty
193argmin:1
194argmax:100
195argvalue:10
196
197arg:FLOAT
198arglabel:Floating gap penalty
199argtype:slider
200argmin:1
201argmax:100
202argvalue:10
203
204in:in1
205informat:flat
206insave:
207
208out:out1
209outformat:flat
210
211
212item:Clustalw DNA Alignment
213itemmethod:(tr '"%//' '>' <in1 >clus_in;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; /bin/rm -f clus_in* in1)
214
215itemhelp:clustal.help
216
217arg:KTUP
218argtype:slider
219arglabel:K-tuple size for fast pairwise search
220argmin:1
221argmax:10
222argvalue:2
223
224arg:WIN
225argtype:slider
226arglabel:Window size for fast pairwise search
227argmin:1
228argmax:10
229argvalue:4
230
231arg:MATRIX_
232argtype:chooser
233arglabel:Weighting matrix
234argchoice:BLOSUM:BLOSUM
235argchoice:PAM:PAM
236argchoice:GONNET:GONNET
237argchoice:ID:ID
238
239arg:FIXED_
240argtype:slider
241arglabel:Gap Open Panelty
242argmin:1
243argmax:100
244argvalue:8.7
245 
246arg:FLOAT_
247arglabel:Gap Extend Panelty
248argtype:slider
249argmin:.001
250argmax:1
251argvalue:.1
252
253
254in:in1
255informat:flat
256insave:
257
258out:out1
259outformat:flat
260
261
262item:Clustalw Protein Alignment
263itemmethod:(tr '"%//' '>' <in1 >clus_in;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;\/bin/rm -f clus_in* in1)
264
265
266itemhelp:clustalw.help
267
268arg:KTUP_
269argtype:slider
270arglabel:K-tuple size for fast pairwise search
271argmin:1
272argmax:10
273argvalue:2
274
275arg:WIN_
276argtype:slider
277arglabel:Window size and top diagonals for fast alignment
278argmin:1
279argmax:10
280argvalue:4
281
282arg:MATRIX_
283argtype:chooser
284arglabel:Weighting matrix
285argchoice:BLOSUM:BLOSUM
286argchoice:PAM:PAM
287argchoice:GONNET:GONNET
288argchoice:ID:ID
289
290arg:FIXED_
291argtype:slider
292arglabel:Gap Open Panelty
293argmin:1
294argmax:100
295argvalue:8.7
296 
297arg:FLOAT_
298arglabel:Gap Extend Panelty
299argtype:slider
300argmin:.001
301argmax:1
302argvalue:.1
303
304
305 
306in:in1
307informat:flat
308insave:
309
310out:out1
311outformat:flat
312
313item:Assemble Contigs
314itemmethod: (tr '"%//' '>' <in1 >in1.tmp;CAP2 in1.tmp $OVERLAP $PMATCH >  out1;/bin/rm -f in1.tmp)
315itemhelp:CAP2.help
316
317arg:OVERLAP
318argtype:slider
319arglabel:Minimum overlap?
320argmin:5
321argmax:100
322argvalue:20
323
324arg:PMATCH
325argtype:slider
326arglabel:Percent match required within overlap
327argmin:25
328argmax:100
329argvalue:90
330
331in:in1
332informat:flat
333
334out:out1
335outformat:gde
336
337
338
339menu:user
340item: Start a slave arb on a foreign host ...
341
342itemmethod: ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait"  &
343
344arg:dis
345argtype:text
346arglabel:hostname of slave host ?
347
348
349 
350
351
352menu:DNA/RNA
353item:Translate...
354itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE $NOSEP in1 > out1
355
356arg:FRAME
357argtype:chooser
358arglabel:Which reading frame?
359argchoice:First:1
360argchoice:Second:2
361argchoice:Third:3
362argchoice:All six:6
363
364arg:MNFRM
365arglabel:Minimum length of NT sequence to translate?
366argtype:slider
367argmin:0
368argmax:500
369argvalue:20
370 
371arg:LTRCODE
372argtype:chooser
373arglabel:Translate to:
374argchoice:Single letter codes:
375argchoice:Triple letter codes:-3
376
377arg:NOSEP
378argtype:chooser
379arglabel: Seperate?
380argchoice:No:
381argchoice:Yes:-sep
382 
383arg:TBL
384arglabel:Codon table?
385argtype:chooser
386argchoice:mycoplasma:2
387argchoice:universal:1
388argchoice:yeast:3
389argchoice:Vert. mito.:4
390
391in:in1
392informat:gde
393 
394out:out1
395outformat:gde
396 
397item:Dot plot
398itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)&
399itemhelp:DotPlotTool.help
400
401in:in1
402informat:gde
403insave:
404
405
406item:Clustal alignment
407itemmethod:(tr '"%//' '>' <in1 >clus_in;cp in1 test; ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; /bin/rm -f clus_in* in1)
408
409itemhelp:clustal_help
410
411arg:KTUP
412argtype:slider
413arglabel:K-tuple size for pairwise search
414argmin:1
415argmax:10
416argvalue:2
417
418arg:WIN
419argtype:slider
420arglabel:Window size
421argmin:1
422argmax:10
423argvalue:4
424
425arg:Trans
426argtype:chooser
427arglabel:Transitions weighted?
428argchoice:Yes:/TRANSIT
429argchoice:No:
430
431arg:FIXED
432argtype:slider
433arglabel:Fixed gap penalty
434argmin:1
435argmax:100
436argvalue:10
437
438arg:FLOAT
439arglabel:Floating gap penalty
440argtype:slider
441argmin:1
442argmax:100
443argvalue:10
444
445
446in:in1
447informat:flat
448insave:
449
450out:out1
451outformat:flat
452
453
454
455item:Variable Positions
456itemmethod:varpos $REV < in1 > out1
457
458arg:REV
459argtype:chooser
460arglabel:Highlight (darken)
461argchoice:Conserved positions:
462argchoice:variable positions:-rev
463
464in:in1
465informat:flat
466
467out:out1
468outformat:colormask
469
470
471
472
473item:MFOLD
474itemmethod:(tr 'a-z' 'A-Z' < seqGB > .GDE.tmp.caps; ZUKERGDE.sh .GDE.tmp.caps $CT $ARBHOME/GDEHELP/ZUKER/ > out1 && $METHOD < out1; Zuk_to_gen < $CT >file.gen; gde file.gen& ${ARB_TEXTEDIT:-textedit} RegionTable )&
475itemhelp:MFOLD.help
476
477in:seqGB
478informat:genbank
479insave:
480
481arg:METHOD
482argtype:chooser
483arglabel:RNA type
484argchoice:Fold Linear RNA:lrna
485argchoice:Fold Circular RNA:crna
486
487arg:CT
488argtype:text
489arglabel:Pairing(ct)  File Name
490argtext:mfold_out
491
492
493item:Draw Secondary structure
494itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) &
495itemhelp:LoopTool.help
496
497arg:TEMPLATE
498argtype:chooser
499arglabel:Use template file ./loop.temp?
500argchoice:No:
501argchoice:Yes:-t loop.temp
502
503in:in1
504informat:genbank
505insave:
506
507
508item:blastn
509itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; blastn $BLASTDB in1.f W=$WORDLEN M=$MATCH N=$MMSCORE > in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1*)&
510itemhelp:blast.help
511
512in:in1
513informat:flat
514insave:
515
516arg:BLASTDB
517argtype:choice_menu
518arglabel:Which Database
519argchoice:genbank:$ARBHOME/GDEHELP/BLAST/genbank
520argchoice:genbank update:$ARBHOME/GDEHELP/BLAST/genupdate
521
522arg:WORDLEN
523argtype:slider
524arglabel:Word Size
525argmin:4
526argmax:18
527argvalue:12
528
529arg:MATCH
530argtype:slider
531arglabel:Match Score
532argmin:1
533argmax:10
534argvalue:5
535
536arg:MMSCORE
537argtype:slider
538arglabel:Mismatch Score
539argmin:-10
540argmax:-1
541argvalue:-5
542
543item:blastx
544itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
545itemhelp:blast.help
546
547in:in1
548informat:flat
549insave:
550
551arg:BLASTDB
552argtype:choice_menu
553arglabel:Which Database
554argchoice:pir1:$ARBHOME/GDEHELP/BLAST/pir
555argchoice:genpept:$ARBHOME/GDEHELP/BLAST/genpept
556
557arg:WORDLEN
558argtype:slider
559arglabel:Word Size
560argmin:1
561argmax:5
562argvalue:3
563
564arg:Matrix
565arglabel:Substitution Matrix:
566argtype:choice_menu
567argchoice:PAM120:PAM120
568argchoice:PAM250:PAM250
569
570arg:CODE
571argtype:choice_menu
572arglabel:Genetic Code
573argchoice:Standard or Universal:0
574argchoice:Vertebrate Mitochondrial:1
575argchoice:Yeast Mitochondrial:2
576argchoice:Mold Mitochondrial and Mycoplasma:3
577argchoice:Invertebrate Mitochondrial:4
578argchoice:Ciliate Macronuclear:5
579argchoice:Protozoan Mitochondrial:6
580argchoice:Plant Mitochondrial:7
581argchoice:Echinodermate Mitochondrial:8
582
583
584item:FASTA (DNA/RNA)
585itemmethod:(sed "s/[//%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; ${ARB_TEXTEDIT:-textedit} in1.out;\rm in1*) &
586itemhelp:FASTA.help
587
588in:in1
589informat:flat
590
591arg:DBASE
592argtype:choice_menu
593arglabel:Database
594argchoice:GenBank Primate:$ARBHOME/GDEHELP/FASTA/GENBANK/gbpri.seq\ 1
595argchoice:GenBank Rodent:$ARBHOME/GDEHELP/FASTA/GENBANK/gbrod.seq\ 1
596argchoice:GenBank all Mammal:$ARBHOME/GDEHELP/FASTA/GENBANK/gbmam.seq\ 1
597argchoice:GenBank verteBrates:$ARBHOME/GDEHELP/FASTA/GENBANK/gbvrt.seq\ 1
598argchoice:GenBank Inverts:$ARBHOME/GDEHELP/FASTA/GENBANK/gbinv.seq\ 1
599argchoice:GenBank pLants:$ARBHOME/GDEHELP/FASTA/GENBANK/gbpln.seq\ 1
600argchoice:GenBank Struct RNA:$ARBHOME/GDEHELP/FASTA/GENBANK/gbrna.seq\ 1
601argchoice:GenBank euk. Organelles:$ARBHOME/GDEHELP/FASTA/GENBANK/gborg.seq\ 1
602argchoice:GenBank phaGe:$ARBHOME/GDEHELP/FASTA/GENBANK/gbphg.seq\ 1
603argchoice:GenBank bacTeria:$ARBHOME/GDEHELP/FASTA/GENBANK/gbbct.seq\ 1
604argchoice:GenBank sYnthetic:$ARBHOME/GDEHELP/FASTA/GENBANK/gbsyn.seq\ 1
605argchoice:GenBank Viral:$ARBHOME/GDEHELP/FASTA/GENBANK/gbvrl.seq\ 1
606argchoice:GenBank Unannotated:$ARBHOME/GDEHELP/FASTA/GENBANK/gbuna.seq\ 1
607
608arg:NUMOFALN
609argtype:slider
610arglabel:Number of Alignment to Report
611argmin:1
612argmax:100
613argvalue:20
614
615arg:MATRIX
616arglabel:Which SMATRIX
617argtype:choice_menu
618argchoice:Default:
619argchoice:altdiag.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/altdiag.mat
620argchoice:altprot.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/altprot.mat
621argchoice:dna.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/dna.mat
622argchoice:prot.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/prot.mat
623
624
625menu:Protein
626item:Clustal Protein Alignment
627itemmethod:(tr '"%//' '>' <in1 >clus_in;cp in1 test; ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; /bin/rm -f clus_in* in1)
628
629
630itemhelp:clustal_help
631
632arg:KTUP
633argtype:slider
634arglabel:K-tuple size for pairwise search
635argmin:1
636argmax:10
637argvalue:2
638
639arg:WIN
640argtype:slider
641arglabel:Window size
642argmin:1
643argmax:10
644argvalue:4
645
646arg:Matrx
647argtype:chooser
648arglabel:Weighting matrix
649argchoice:PAM 250:PAM250
650argchoice:PAM 100:PAM100
651argchoice:Identity:ID
652
653arg:FIXED
654argtype:slider
655arglabel:Fixed gap penalty
656argmin:1
657argmax:100
658argvalue:10
659 
660arg:FLOAT
661arglabel:Floating gap penalty
662argtype:slider
663argmin:1
664argmax:100
665argvalue:10
666
667
668 
669in:in1
670informat:flat
671insave:
672
673out:out1
674outformat:flat
675
676item:blastp
677itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
678itemhelp:blast.help
679
680in:in1
681informat:flat
682insave:
683
684arg:BLASTDB
685argtype:choice_menu
686arglabel:Which Database
687argchoice:pir:$ARBHOME/GDEHELP/BLAST/pir
688argchoice:genpept:$ARBHOME/GDEHELP/BLAST/genpept
689argchoice:local:$ARBHOME/GDEHELP/BLAST/local_db
690
691arg:Matrix
692arglabel:Substitution Matrix:
693argtype:choice_menu
694argchoice:PAM120:PAM120
695argchoice:PAM250:PAM250
696
697arg:WORDLEN
698argtype:slider
699arglabel:Word Size
700argmin:1
701argmax:5
702argvalue:3
703
704item:tblastn
705itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
706itemhelp:blast.help
707
708in:in1
709informat:flat
710insave:
711
712arg:BLASTDB
713argtype:choice_menu
714arglabel:Which Database
715argchoice:genbank:$ARBHOME/GDEHELP/BLAST/genbank
716argchoice:genbank update:$ARBHOME/GDEHELP/BLAST/genupdate
717
718arg:Matrix
719arglabel:Substitution Matrix:
720argtype:choice_menu
721argchoice:PAM120:PAM120
722argchoice:PAM250:PAM250
723
724arg:WORDLEN
725argtype:slider
726arglabel:Word Size
727argmin:4
728argmax:18
729argvalue:12
730
731arg:CODE
732argtype:choice_menu
733arglabel:Genetic Code
734argchoice:Standard or Universal:0
735argchoice:Vertebrate Mitochondrial:1
736argchoice:Yeast Mitochondrial:2
737argchoice:Mold Mitochondrial and Mycoplasma:3
738argchoice:Invertebrate Mitochondrial:4
739argchoice:Ciliate Macronuclear:5
740argchoice:Protozoan Mitochondrial:6
741argchoice:Plant Mitochondrial:7
742argchoice:Echinodermate Mitochondrial:8
743
744item:blast3
745itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
746itemhelp:blast3.help
747
748in:in1
749informat:flat
750insave:
751
752arg:BLASTDB
753argtype:choice_menu
754arglabel:Which Database
755argchoice:pir1:$ARBHOME/GDEHELP/BLAST/pir
756argchoice:genpept:$ARBHOME/GDEHELP/BLAST/genpept
757
758arg:Matrix
759arglabel:Substitution Matrix:
760argtype:choice_menu
761argchoice:PAM120:PAM120
762argchoice:PAM250:PAM250
763
764arg:WORDLEN
765argtype:slider
766arglabel:Word Size
767argmin:1
768argmax:5
769argvalue:3
770
771item:FASTA (Protein)
772itemmethod:(sed "s/[//%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; ${ARB_TEXTEDIT:-textedit} in1.out;\rm in1*) &
773itemhelp:FASTA.help
774
775in:in1
776informat:flat
777
778arg:DBASE
779argtype:choice_menu
780arglabel:Database
781argchoice:NBRF PIR1:$ARBHOME/GDEHELP/FASTA/PIR/pir1.dat\ 2
782argchoice:NBRF PIR2:$ARBHOME/GDEHELP/FASTA/PIR/pir2.dat\ 2
783argchoice:NBRF PIR3:$ARBHOME/GDEHELP/FASTA/PIR/pir3.dat\ 2
784
785
786arg:NUMOFALN
787argtype:slider
788arglabel:Number of Alignment to Report
789argmin:1
790argmax:100
791argvalue:20
792
793arg:MATRIX
794arglabel:Which SMATRIX
795argtype:choice_menu
796argchoice:Default:
797argchoice:Minimum mutation matrix:-s $ARBHOME/GDEHELP/FASTA/MATRIX/codaa.mat
798argchoice:Identity matrix:-s $ARBHOME/GDEHELP/FASTA/MATRIX/idnaa.mat
799argchoice:Identity matrix for mismatches:-s $ARBHOME/GDEHELP/FASTA/MATRIX/idpaa.mat
800argchoice:PAM250:-s $ARBHOME/GDEHELP/FASTA/MATRIX/pam250.mat
801argchoice:PAM120:-s $ARBHOME/GDEHELP/FASTA/MATRIX/pam120.mat
802
803
804
805menu:Seq management
806item:Assemble Contigs
807itemmethod:(sed "s////>/"<in1 >in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp)
808itemhelp:CAP2.help
809
810arg:OVERLAP
811argtype:slider
812arglabel:Minimum overlap?
813argmin:5
814argmax:100
815argvalue:20
816
817arg:PMATCH
818argtype:slider
819arglabel:Percent match required within overlap
820argmin:25
821argmax:100
822argvalue:90
823
824in:in1
825informat:flat
826
827out:out1
828outformat:gde
829outoverwrite:
830
831item:Map View
832itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)&
833itemhelp:mapview.help
834
835in:in1
836informat:gde
837insave:
838
839arg:PBL
840arglabel:Pixel Between Lines
841argtype:slider
842argvalue:10
843argmin:1
844argmax:15
845
846arg:NPP
847arglabel:Nucleotides Per Pixel
848argtype:slider
849argvalue:1
850argmin:1
851argmax:20
852
853arg:LWIDTH
854arglabel:Line Thickness
855argtype:slider
856argvalue:2
857argmin:1
858argmax:5
859
860
861item:Restriction sites
862itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp; cp out1 tmp );
863itemhelp:Restriction.help
864
865arg:ENZ
866argtype:text
867arglabel:Enzyme file
868argtext:$ARBHOME/GDEHELP/DATA_FILES/enzymes
869
870arg:PRE_EDIT
871argtype:chooser
872arglabel:Edit enzyme file first?
873argchoice:Yes:${ARB_TEXTEDIT:-textedit} in1.tmp;
874argchoice:No:
875
876in:in1
877informat:flat
878
879out:out1
880outformat:colormask
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902menu:SAI
903item:Positional Variability by Olsons dnamlrates (max 5000 Species, 8000 seqlength)
904itemmethod:(/bin/rm -f outfile infile treefile ;(echo C F M T U L;echo C 35; echo M 10; echo T 2.0 ) |arb_convert_aln -GenBank in1 -phylip2 in1.ph;echo 1 >>in1.ph; arb_export_tree $TREE >>in1.ph;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;echo done )&
905itemhelp:phylip.help
906
907arg:TREE
908argtype:tree
909arglabel:Base Tree
910argchoice:tree_main
911
912in:in1
913informat:genbank
914inmask:
915insave:
916
917
918menu:Incremental_Phylogeny
919item:FastDnaMl (max 500 Species) ...
920itemmethod:(/bin/rm -f outfile infile treefile ;(echo Y F Q G T R "`arb_export_rates $RATES`";echo G 0 0; echo T 2.0 ) |arb_convert_aln -GenBank in1 -phylip2 infile;arb_export_tree $TREE >>infile;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; rm in1 )&
921itemhelp:phylip.help
922
923arg:RATES
924argtype:weights
925arglabel:Select a Weighting Mask
926argchoice:POS_VAR_BY_PARS
927
928arg:TREE
929argtype:tree
930arglabel:Base Tree
931argchoice:tree_main
932
933arg:DISPLAY_FUNC
934argtype:chooser
935arglabel:What to do with the tree:?
936argchoice:ARB ('tree_fml_//'):arb_read_tree tree_fml_$$ treefile "PRG=FASTDNAML FILTER=$FILTER PKG=olsen/felsenstein RATE=$RATES"
937argchoice:Treetool:treetool treefile
938
939
940in:in1
941informat:genbank
942inmask:
943insave:
944
945
946menu:Phylogeny
947item:DeSoete Tree fit
948itemmethod: ( ${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;/bin/rm -f in1* )&
949itemhelp:lsadt.help
950
951in:in1
952informat:genbank
953insave:
954inmask:
955
956arg:CORR
957arglabel:Dist. correction?
958argtype:chooser
959argchoice:Olsen:-c=olsen
960argchoice:Jukes/Cantor:-c=jukes
961argchoice:None:-c=none
962
963arg:INIT
964arglabel:Parameter estimate
965argtype:choice_menu
966argchoice:uniformly distributed random numbers:1
967argchoice:error-perturbed data:2
968argchoice:original distance data from input matrix:3
969
970arg:SEED
971argtype:slider
972arglabel:Random nr. seed
973argmin:0
974argmax:65535
975argvalue:12345
976 
977arg:DISPLAY_FUNC
978argtype:chooser
979arglabel:View tree using
980argchoice:ARB ('tree_desoete'):arb_read_tree tree_desoete_$$ in1.out "PRG=DeSoete CORR=$CORR FILTER=$FILTER"
981argchoice:TextEdit:${ARB_TEXTEDIT:-textedit} in1.out
982argchoice:Treetool:treetool in1.out
983
984item:Phylip Distance Methods ( Original Phylip, Interactiv )
985itemmethod:(    /bin/rm -f treefile infile outfile; arb_convert_aln -GenBank  in1  -phylip infile ;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;        /bin/rm -f  in1  infile outfile treefile        )&
986 
987arg:DISPLAY_FUNC
988argtype:chooser
989arglabel:What to do with the tree:?
990argchoice:ARB ('tree_ph_xxx'):(arb_read_tree tree_ph_$$ treefile "FILTER=$FILTER PKG=phylip")
991argchoice:TextEdit:${ARB_TEXTEDIT:-textedit} outfile
992argchoice:Treetool:treetool treefile
993
994arg:PROGRAM
995arglabel:Which method?
996argtype:chooser
997argchoice:DNADIST:mv -f infile outfile
998argchoice:Fitch:${ARB_XCMD:-cmdtool} fitch
999argchoice:Kitsch:${ARB_XCMD:-cmdtool} kitsch
1000argchoice:Neighbor:${ARB_XCMD:-cmdtool} neighbor
1001
1002arg:DPGM
1003arglabel:Treat data as..
1004argtype:chooser
1005argchoice:DNA:dnadist
1006argchoice:RNA:dnadist
1007argchoice:AA:protdist
1008
1009
1010in:in1
1011informat:genbank
1012inmask:sdfgdfg
1013insave:
1014
1015
1016 
1017 
1018
1019item:Phylip Distance Methods ( Simple GUI Based Interface )
1020itemmethod:(    /bin/rm -f treefile infile outfile; arb_convert_aln -GenBank  in1  -phylip infile ;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;        /bin/rm -f  in1  infile outfile treefile        )&
1021itemhelp:phylip.help
1022 
1023arg:DISPLAY_FUNC
1024argtype:chooser
1025arglabel:What to do with the tree:?
1026argchoice:ARB ('tree_ph_xxx'):($CORRECTION;echo||$DPGM;arb_read_tree tree_ph_$$ treefile "PRG=$PROGRAM CORR=$TEXT FILTER=$FILTER PKG=phylip")
1027argchoice:TextEdit:${ARB_TEXTEDIT:-textedit} outfile
1028argchoice:Treetool:treetool treefile
1029
1030arg:PROGRAM
1031arglabel:Which method?
1032argtype:chooser
1033argchoice:Neighbor:neighbor
1034argchoice:Fitch:fitch
1035argchoice:Kitsch:kitsch
1036
1037arg:DPGM
1038arglabel:Treat data as..
1039argtype:chooser
1040argchoice:DNA/RNA:(arb_echo $DNAFLAGS |dnadist);TEXT=$DNATEXT
1041argchoice:AA:(arb_echo $PROFLAGS |protdist);TEXT=$PROTEXT
1042
1043arg:CORRECTION
1044arglabel:Correction DNA/PROT
1045argtype:chooser
1046argchoice:Kimura  / Dayhoff:            DNATEXT=kimura;         DNAFLAGS="y";           PROTEXT=dayhoff;        PROFLAGS="y"
1047argchoice:Jin_Nei / Kimura:             DNATTEXT=jinnai;        DNAFLAGS="d y";         PROTEXT=kimura;         PROFLAGS="p y"
1048argchoice:Max.Lik./(George/Hunt/Barker):DNATEXT=maxlik;         DNAFLAGS="d d y";       PROTEXT=ghb;            PROFLAGS="p p y"
1049argchoice:JukesC. / Chemical:           DNATEXT=jc;             DNAFLAGS="d d d y";     PROTEXT=chemical;       PROFLAGS="p p a c y"
1050argchoice:JukesC. / Hall:               DNATEXT=jc;             DNAFLAGS="d d d y";     PROTEXT=hall;           PROFLAGS="p p a h y"
1051argchoice:USER    / USER:               DNATEXT=user;           DNAFLAGS="";            PROTEXT=user;           PROFLAGS=""
1052
1053
1054
1055in:in1
1056informat:genbank
1057inmask:
1058insave:
1059
1060
1061item:Phylip Distance Matrix
1062itemmethod:(/bin/rm -f treefile infile outfile; arb_convert_aln -GenBank in1 -phylip infile ; $PREEDIT ${ARB_XCMD:-cmdtool} $DPGM;${ARB_TEXTEDIT:-textedit} outfile;/bin/rm -f in1 infile outfile)&
1063itemhelp:phylip.help
1064 
1065arg:DPGM
1066arglabel:Treat data as..
1067argtype:chooser
1068argchoice:DNA/RNA:dnadist
1069argchoice:AA:protdist
1070
1071arg:PREEDIT
1072argtype:chooser
1073arglabel:Edit input before running?
1074argchoice:No:
1075argchoice:Yes:${ARB_TEXTEDIT:-textedit} infile;
1076 
1077in:in1
1078informat:genbank
1079inmask:
1080insave:
1081
1082
1083item:Phylip Parsimony/M.L.
1084 
1085itemmethod:(/bin/rm -f treefile infile outfile; arb_convert_aln -GenBank  in1  -phylip infile ;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;/bin/rm -f  in1  infile outfile treefile  )&
1086itemhelp:phylip.help
1087
1088arg:DISPLAY_FUNC
1089argtype:chooser
1090arglabel:What to do with the tree:?
1091argchoice:ARB ('tree_phylip'):arb_read_tree $CONSFLAG tree_ph_$$ treefile "PRG=$PROGRAM FILTER=$FILTER PKG=phylip"
1092argchoice:TextEdit:arb_textedit outfile
1093argchoice:Treetool:treetool treefile
1094 
1095arg:BOOTSTRP
1096arglabel:How many bootstraps ?
1097argtype:chooser
1098argchoice:Do not bootstrap:CONSFLAG=;arb_echo y |$PROGRAM
1099argchoice:10: arb_echo 1 r 10 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 10 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
1100argchoice:100: arb_echo 1 r 100 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 100 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
1101argchoice:1000: arb_echo 1 r 1000 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 1000 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
1102
1103arg:PROGRAM
1104argtype:chooser
1105arglabel:Which program to run?
1106argchoice:DNAPARS:dnapars
1107 
1108 
1109argchoice:DNACOMP:dnacomp
1110 
1111argchoice:DNAINVAR:dnainvar
1112argchoice:PROTPARS:protpars
1113 
1114
1115
1116
1117in:in1
1118informat:genbank
1119inmask:
1120insave:
1121
1122
1123item:DNA_ML (FastDnaMl) (max 150 Species)
1124itemmethod:(/bin/rm -f outfile infile treefile ;echo Y F "`arb_export_rates $RATES`" |arb_convert_aln -GenBank in1 -phylip2 infile;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ; rm in1 )&
1125itemhelp:phylip.help
1126
1127arg:RATES
1128argtype:weights
1129arglabel:Select a Weighting Mask
1130argchoice:POS_VAR_BY_PARS
1131
1132arg:DISPLAY_FUNC
1133argtype:chooser
1134arglabel:What to do with the tree:?
1135argchoice:ARB ('tree_fml_//'):arb_read_tree tree_fml_$$ treefile "PRG=FASTDNAML FILTER=$FILTER PKG=olsen/felsenstein RATE=$RATES"
1136argchoice:Treetool:treetool treefile
1137
1138in:in1
1139informat:genbank
1140inmask:
1141insave:
1142
1143
1144item:Protein_ML (molphy max 40 species)
1145 
1146itemmethod:(/bin/rm -f treefile infile outfile; arb_convert_aln -GenBank  in1  -phylip infile ;cat infile |tr '?' '-' >in1.in;${ARB_XCMD:-cmdtool} sh -c "LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb}";export LD_LIBRARY_PATH; item_command ;arb_wait" ;/bin/rm -f  in1  infile outfile treefile  )&
1147itemhelp:phylip.help
1148
1149arg:DISPLAY_FUNC
1150argtype:chooser
1151arglabel:What to do with the tree:?
1152argchoice:ARB ('tree_phylip'):arb_read_tree $CONSFLAG tree_ph_$$ protml.tre "PRG=protml PARMETERS=$MODEL$SEARCH FILTER=$FILTER PKG=molphy"
1153argchoice:TextEdit:arb_textedit outfile
1154argchoice:Treetool:treetool treefile
1155 
1156arg:BOOTSTRP
1157arglabel:How many bootstraps ?
1158argtype:chooser
1159argchoice:Do not bootstrap:CONSFLAG=;protml $MODEL $SEARCH -v -I in1.in
1160argchoice:10: arb_echo 1 r 10 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 10 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
1161argchoice:100: arb_echo 1 r 100 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 100 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
1162argchoice:1000: arb_echo 1 r 1000 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 1000 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile
1163
1164arg:MODEL
1165argtype:chooser
1166arglabel:Which model to use ?
1167argchoice:JTT:-j
1168argchoice:Dayhoff:-d
1169argchoice:mtREV24:-m
1170argchoice:Poisson:-p
1171argchoice:Jones Tayler & Thornton:-jf
1172argchoice:Dayhoff-F:-df
1173argchoice:Adachi & Hasegawa(1995):-mf
1174
1175arg:SEARCH
1176argtype:chooser
1177arglabel:Search Strategie
1178argchoice:star decomposition:-s
1179argchoice:exhaustive:-e
1180argchoice:quickadd:-q
1181
1182in:in1
1183informat:genbank
1184inmask:
1185insave:
1186
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