fix: use original SunOS menus
This commit is contained in:
parent
416ce85007
commit
d16e0470a1
3 changed files with 2642 additions and 170 deletions
826
CORE/.GDEmenus
826
CORE/.GDEmenus
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@ -1,7 +1,7 @@
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1menu:File
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menu:File
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item:test cmask output
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itemmethod: kedit in1
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itemmethod: textedit in1
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in:in1
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informat:colormask
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@ -44,9 +44,6 @@ itemhelp:readseq.help
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arg:FORMAT
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argtype:choice_list
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argchoice:FASTA:8
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argchoice:NEXUS:17
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argchoice:Phylip v3.3:12
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argchoice:IG/Stanford:1
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argchoice:GenBank:2
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argchoice:NBRF:3
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@ -206,7 +203,7 @@ informat:gde
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insave:
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item:Clustal alignment
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itemmethod:(tr '%#' '>'<in1>clus_in;clustalw -quicktree -output=PIR -infile=clus_in -align > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1;/bin/rm -f clus_in* in1* )&
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itemmethod:(tr '%#' '>'<in1>clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Trans /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1; /bin/rm -f clus_in* in1* )&
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itemhelp:clustal_help
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@ -248,7 +245,7 @@ arg:REPORT
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argtype:chooser
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arglabel:View assembly report?
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argchoice:No:
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argchoice:Yes:kedit in1.rpt&
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argchoice:Yes:textedit in1.rpt&
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in:in1
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@ -270,25 +267,6 @@ informat:flat
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out:out1
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outformat:colormask
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item:Phrap
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itemmethod:readseq in1 -a -f8 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp; phrap OUTPUTFILE; readseq -a -f2 OUTPUTFILE.contigs > out1;/bin/rm -rf OUTPUT*;
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in:in1
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informat:genbank
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out:out1
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outformat:genbank
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item:SNAP
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itemmethod: cat in1 > infile;/usr/local/bio/GDE/bin/fasta2snap.pl > outfile; /usr/bin/X11/xterm -e /home/tulio/bio/SNAP/SNAP.pl outfile; kedit backg*; kedit summ*; sheeltool /home/tulio/bio/codons-xyplot.pl codons.*; kedit codon.data; /bin/rm -rf back* codon* summ*;
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in:in1
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informat:flat
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out:out1
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outformat:text
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item:Find all <meta-f>
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itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1;
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@ -381,19 +359,66 @@ out:out1
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outformat:gde
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item:MFOLD
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itemmethod:(tr 'a-z' 'A-Z' < seqGB > .GDE.tmp.caps; ZUKERGDE.sh .GDE.tmp.caps $CT $GDE_HELP_DIR/ZUKER/ > out1 && $METHOD < out1; Zuk_to_gen < $CT >file.gen; gde file.gen& textedit RegionTable; /bin/rm -f RegionTable out1 seqGB* .GDE.tmp.caps)&
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itemhelp:MFOLD.help
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in:seqGB
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informat:genbank
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insave:
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arg:METHOD
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argtype:chooser
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arglabel:RNA type
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argchoice:Fold Linear RNA:lrna
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argchoice:Fold Circular RNA:crna
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arg:CT
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argtype:text
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arglabel:Pairing(ct) File Name
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argtext:mfold_out
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item:Draw Secondary structure
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itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) &
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itemhelp:LoopTool.help
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arg:TEMPLATE
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argtype:chooser
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arglabel:Use template file ./loop.temp?
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argchoice:No:
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argchoice:Yes:-t loop.temp
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in:in1
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informat:genbank
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insave:
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item:Highlight helix
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itemmethod:readseq -a -f8 in1 | sed "s/>HELIX/\"HELIX/" > in1.flat; sho_helix < in1.flat > out1;rm in1.flat
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itemhelp:sho_helix.help
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in:in1
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informat:genbank
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out:out1
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outformat:colormask
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#Menu for DNA/RNA
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item:blastn
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; /usr/local/bio/blast/blastall -p blastn -d $BLASTDBDNA -i in1.f -W $WORDLEN -M $MATCH > in1.tmp; kedit in1.tmp; rm in1*)&
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; blastn $BLASTDB in1.f W=$WORDLEN M=$MATCH N=$MMSCORE > in1.tmp; textedit in1.tmp; rm in1*)&
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in:in1
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informat:flat
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insave:
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arg:BLASTDBDNA
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arg:BLASTDB
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argtype:choice_list
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arglabel:Which Database
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argchoice:HIV-1 Seq. Db.:/usr/local/bio/db/DNA/hiv17-08-01.fasta2
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argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank
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argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate
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arg:WORDLEN
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argtype:slider
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arglabel:Word Size
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@ -416,18 +441,16 @@ argmax:-1
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argvalue:-5
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item:blastx
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; /usr/local/bio/blast/blastall -p blastx -d $BLASTDB -i in1.f -W $WORDLEN -M PAM30 > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1*)&
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; textedit in1.tmp; rm in1* PAM???)&
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in:in1
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informat:flat
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insave:
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arg:BLASTDBDNA
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arg:BLASTDB
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argtype:choice_list
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arglabel:Which Database
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argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta
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argchoice:pir1:$GDE_HELP_DIR/BLAST/pir
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argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
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arg:WORDLEN
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@ -440,13 +463,12 @@ argvalue:3
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arg:Matrix
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arglabel:Substitution Matrix:
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argtype:choice_list
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argchoice:PAM30:PAM30
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argchoice:PAM70:PAM70
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argchoice:PAM120:PAM120
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argchoice:PAM250:PAM250
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arg:CODE
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argtype:choice_list
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arglabel:Genetic Code
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argchoice:Standard or Universal:0
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argchoice:Vertebrate Mitochondrial:1
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argchoice:Yeast Mitochondrial:2
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@ -457,57 +479,119 @@ argchoice:Protozoan Mitochondrial:6
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argchoice:Plant Mitochondrial:7
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argchoice:Echinodermate Mitochondrial:8
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item:------------------------
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item:Add a new DNA blast db
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itemmethod:xterm -e formatdb -i $sourcefile -p F -o T; /usr/local/bio/GDE/bin/installBLASTDB.pl $sourcefile $menuname;
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item:FASTA (DNA/RNA)
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itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) &
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itemhelp:FASTA.help
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arg:sourcefile
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argtype:text
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arglabel: enter the file name
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in:in1
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informat:flat
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arg:menuname
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argtype:text
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arglabel: enter the name of the DB
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arg:DBASE
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argtype:choice_list
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arglabel:Database
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argchoice:GenBank Primate:$GDE_HELP_DIR/FASTA/GENBANK/gbpri.seq\ 1
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argchoice:GenBank Rodent:$GDE_HELP_DIR/FASTA/GENBANK/gbrod.seq\ 1
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argchoice:GenBank all Mammal:$GDE_HELP_DIR/FASTA/GENBANK/gbmam.seq\ 1
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argchoice:GenBank verteBrates:$GDE_HELP_DIR/FASTA/GENBANK/gbvrt.seq\ 1
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argchoice:GenBank Inverts:$GDE_HELP_DIR/FASTA/GENBANK/gbinv.seq\ 1
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argchoice:GenBank pLants:$GDE_HELP_DIR/FASTA/GENBANK/gbpln.seq\ 1
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argchoice:GenBank Struct RNA:$GDE_HELP_DIR/FASTA/GENBANK/gbrna.seq\ 1
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argchoice:GenBank euk. Organelles:$GDE_HELP_DIR/FASTA/GENBANK/gborg.seq\ 1
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argchoice:GenBank phaGe:$GDE_HELP_DIR/FASTA/GENBANK/gbphg.seq\ 1
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argchoice:GenBank bacTeria:$GDE_HELP_DIR/FASTA/GENBANK/gbbct.seq\ 1
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argchoice:GenBank sYnthetic:$GDE_HELP_DIR/FASTA/GENBANK/gbsyn.seq\ 1
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argchoice:GenBank Viral:$GDE_HELP_DIR/FASTA/GENBANK/gbvrl.seq\ 1
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argchoice:GenBank Unannotated:$GDE_HELP_DIR/FASTA/GENBANK/gbuna.seq\ 1
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arg:NUMOFALN
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argtype:slider
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arglabel:Number of Alignment to Report
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argmin:1
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argmax:100
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argvalue:20
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#Sequence dataset
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menu:seq. datasets
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arg:MATRIX
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arglabel:Which SMATRIX
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argtype:choice_list
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argchoice:Default:
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argchoice:altdiag.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altdiag.mat
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argchoice:altprot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altprot.mat
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argchoice:dna.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/dna.mat
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argchoice:prot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/prot.mat
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menu:Protein
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item:-------------
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item:add a new dataset
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itemmethod:mkdir db; cp $file db/ ;xterm -e /usr/local/bio/GDE/newDATASET.pl $name $file
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item:Clustal Protein Alignment
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itemmethod:(tr '%#"' '>' <in1>clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Matrx /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>P1;/%/g" < clus_in.pir > in1;$REPORT gde in1;/bin/rm -f in1* clus_in* )&
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itemhelp:clustal_help
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arg:name
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argtype:text
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arglabel:Enter the dataset name ?
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arg:KTUP
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argtype:slider
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arglabel:K-tuple size for pairwise search
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argmin:1
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argmax:10
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argvalue:2
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arg:file
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argtype:text
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arglabel:Enter the dataset file (in FASTA) ?
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arg:WIN
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argtype:slider
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arglabel:Window size
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argmin:1
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argmax:10
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argvalue:4
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arg:Matrx
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argtype:chooser
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arglabel:Weighting matrix
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argchoice:PAM 250:PAM250
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argchoice:PAM 100:PAM100
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argchoice:Identity:ID
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#Menu for Protein
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menu:protein
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item:blastp
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp /usr/local/bio/db/PAM30; /usr/local/bio/blast/blastall -p blastp -d $BLASTDBPROT -i in1.f -W $WORDLEN -M $Matrix > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1* PAM30)&
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arg:FIXED
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argtype:slider
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arglabel:Fixed gap penalty
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argmin:1
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argmax:100
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argvalue:10
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arg:FLOAT
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arglabel:Floating gap penalty
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argtype:slider
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argmin:1
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argmax:100
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argvalue:10
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arg:REPORT
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argtype:chooser
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arglabel:View assembly report?
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argchoice:No:
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argchoice:Yes:textedit in1.rpt&
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in:in1
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informat:flat
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insave:
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arg:BLASTDBPROT
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#Menu for Protein
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item:blastp
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)&
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in:in1
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informat:flat
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insave:
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arg:BLASTDB
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argtype:choice_list
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arglabel:Which Database
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argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta
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argchoice:pir:$GDE_HELP_DIR/BLAST/pir
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argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
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argchoice:local:$GDE_HELP_DIR/BLAST/local_db
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arg:Matrix
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barglabel:Substitution Matrix:
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arglabel:Substitution Matrix:
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argtype:choice_list
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argchoice:PAM30:PAM30
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argchoice:PAM70:PAM70
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argchoice:PAM120:PAM120
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argchoice:PAM250:PAM250
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arg:WORDLEN
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argtype:slider
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@ -517,7 +601,7 @@ argmax:5
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argvalue:3
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item:tblastn
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp /usr/local/bio/db/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; kedit in1.tmp; rm in1* PAM???)&
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; textedit in1.tmp; rm in1* PAM???)&
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in:in1
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informat:flat
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@ -532,8 +616,8 @@ argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate
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arg:Matrix
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arglabel:Substitution Matrix:
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argtype:choice_list
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argchoice:PAM30:PAM30
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argchoice:PAM70:PAM70
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argchoice:PAM120:PAM120
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argchoice:PAM250:PAM250
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arg:WORDLEN
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argtype:slider
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@ -555,6 +639,90 @@ argchoice:Protozoan Mitochondrial:6
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argchoice:Plant Mitochondrial:7
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argchoice:Echinodermate Mitochondrial:8
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item:blast3
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itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)&
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in:in1
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informat:flat
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insave:
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arg:BLASTDB
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argtype:choice_list
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arglabel:Which Database
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argchoice:pir1:$GDE_HELP_DIR/BLAST/pir
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argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
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arg:Matrix
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arglabel:Substitution Matrix:
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argtype:choice_list
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argchoice:PAM120:PAM120
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argchoice:PAM250:PAM250
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arg:WORDLEN
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argtype:slider
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arglabel:Word Size
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argmin:1
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argmax:5
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argvalue:3
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item:FASTA (Protein)
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itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) &
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itemhelp:FASTA.help
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in:in1
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informat:flat
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arg:DBASE
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argtype:choice_list
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arglabel:Database
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argchoice:NBRF PIR1:$GDE_HELP_DIR/FASTA/PIR/pir1.dat\ 2
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argchoice:NBRF PIR2:$GDE_HELP_DIR/FASTA/PIR/pir2.dat\ 2
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argchoice:NBRF PIR3:$GDE_HELP_DIR/FASTA/PIR/pir3.dat\ 2
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arg:NUMOFALN
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argtype:slider
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arglabel:Number of Alignment to Report
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argmin:1
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argmax:100
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argvalue:20
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arg:MATRIX
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arglabel:Which SMATRIX
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argtype:choice_list
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argchoice:Default:
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argchoice:Minimum mutation matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/codaa.mat
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argchoice:Identity matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/idnaa.mat
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argchoice:Identity matrix for mismatches:-s $GDE_HELP_DIR/FASTA/MATRIX/idpaa.mat
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argchoice:PAM250:-s $GDE_HELP_DIR/FASTA/MATRIX/pam250.mat
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argchoice:PAM120:-s $GDE_HELP_DIR/FASTA/MATRIX/pam120.mat
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menu:Seq management
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item:Assemble Contigs
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itemmethod:(sed "s/#/>/"<in1 >in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp)
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itemhelp:CAP2.help
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arg:OVERLAP
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argtype:slider
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arglabel:Minimum overlap?
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argmin:5
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argmax:100
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argvalue:20
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arg:PMATCH
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argtype:slider
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arglabel:Percent match required within overlap
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argmin:25
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argmax:100
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argvalue:90
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in:in1
|
||||
informat:flat
|
||||
|
||||
out:out1
|
||||
outformat:gde
|
||||
outoverwrite:
|
||||
|
||||
item:Map View
|
||||
itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)&
|
||||
|
|
@ -585,69 +753,114 @@ argvalue:2
|
|||
argmin:1
|
||||
argmax:5
|
||||
|
||||
item:--------------------------
|
||||
item:Add a new Protein blast db
|
||||
itemmethod:xterm -e formatdb -i $sourcefile -p T -o T; /usr/local/bio/GDE/bin/installBLASTDBPROT.pl $sourcefile $menuname;
|
||||
|
||||
arg:sourcefile
|
||||
item:Restriction sites
|
||||
itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp);
|
||||
itemhelp:Restriction.help
|
||||
|
||||
arg:ENZ
|
||||
argtype:text
|
||||
arglabel: Enter the file (in FASTA)
|
||||
arglabel:Enzyme file
|
||||
argtext:$GDE_HELP_DIR/DATA_FILES/enzymes
|
||||
|
||||
arg:menuname
|
||||
argtype:text
|
||||
arglabel: Enter the name of the DB
|
||||
arg:PRE_EDIT
|
||||
argtype:chooser
|
||||
arglabel:Edit enzyme file first?
|
||||
argchoice:Yes:textedit in1.tmp;
|
||||
argchoice:No:
|
||||
|
||||
#Phylogenetic Menu
|
||||
in:in1
|
||||
informat:flat
|
||||
|
||||
out:out1
|
||||
outformat:colormask
|
||||
|
||||
menu:Phylogeny
|
||||
|
||||
item:DeSoete Tree fit
|
||||
itemmethod: (readseq -a -f8 in1>in1.flat;count -t $CORR in1.flat> in1.tmp ; lsadt<in1.tmp -seed $SEED -init $INIT -empty -99.9 > in1.out ; $DISPLAY_FUNC in1.out;/bin/rm -f in1* )&
|
||||
itemhelp:lsadt.help
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
insave:
|
||||
inmask:
|
||||
|
||||
arg:CORR
|
||||
arglabel:Distance correction?
|
||||
argtype:chooser
|
||||
argchoice:Olsen:-c=olsen
|
||||
argchoice:Jukes/Cantor:-c=jukes
|
||||
argchoice:None:-c=none
|
||||
|
||||
arg:INIT
|
||||
arglabel:Initial parameter estimate
|
||||
argtype:choice_list
|
||||
argchoice:uniformly distributed random numbers:1
|
||||
argchoice:error-perturbed data:2
|
||||
argchoice:original distance data from input matrix:3
|
||||
|
||||
arg:SEED
|
||||
argtype:slider
|
||||
arglabel:Random number seed
|
||||
argmin:0
|
||||
argmax:65535
|
||||
argvalue:12345
|
||||
|
||||
arg:DISPLAY_FUNC
|
||||
argtype:chooser
|
||||
arglabel:View tree using
|
||||
argchoice:TextEdit:textedit
|
||||
argchoice:Treetool:treetool <
|
||||
|
||||
item:Phylip help
|
||||
itemmethod:(netscape /usr/local/bio/phylip/doc/$FILE)&
|
||||
itemmethod:(textedit $GDE_HELP_DIR/PHYLIP/$FILE)&
|
||||
|
||||
arg:FILE
|
||||
argtype:choice_list
|
||||
arglabel:Which program?
|
||||
argchoice:clique:clique.html
|
||||
argchoice:consense:consense.html
|
||||
argchoice:contchar:contchar.html
|
||||
argchoice:contml:contml.html
|
||||
argchoice:contrast:contrast.html
|
||||
argchoice:discrete:discrete.html
|
||||
argchoice:distance:distance.html
|
||||
argchoice:dnaboot:dnaboot.html
|
||||
argchoice:dnacomp:dnacomp.html
|
||||
argchoice:dnadist:dnadist.html
|
||||
argchoice:dnainvar:dnainvar.html
|
||||
argchoice:dnaml:dnaml.html
|
||||
argchoice:dnamlk:dnamlk.html
|
||||
argchoice:dnamove:dnamove.html
|
||||
argchoice:dnapars:dnapars.html
|
||||
argchoice:dnapenny:dnapenny.html
|
||||
argchoice:dollop:dollop.html
|
||||
argchoice:dolmove:dolmove.html
|
||||
argchoice:dolpenny:dolpenny.html
|
||||
argchoice:draw:draw.html
|
||||
argchoice:drawgram:drawgram.html
|
||||
argchoice:drawtree:drawtree.html
|
||||
argchoice:factor:factor.html
|
||||
argchoice:fitch:fitch.html
|
||||
argchoice:gendist:gendist.html
|
||||
argchoice:kitsch:kitsch.html
|
||||
argchoice:main:main.html
|
||||
argchoice:mix:mix.html
|
||||
argchoice:move:move.html
|
||||
argchoice:neighbor:neighbor.html
|
||||
argchoice:penny:penny.html
|
||||
argchoice:protpars:protpars.html
|
||||
argchoice:read.me.general:read.me.general.html
|
||||
argchoice:restml:restml.html
|
||||
argchoice:seqboot:seqboot.html
|
||||
argchoice:sequence:sequence.html
|
||||
argchoice:boot:boot.doc
|
||||
argchoice:clique:clique.doc
|
||||
argchoice:consense:consense.doc
|
||||
argchoice:contchar:contchar.doc
|
||||
argchoice:contml:contml.doc
|
||||
argchoice:contrast:contrast.doc
|
||||
argchoice:discrete:discrete.doc
|
||||
argchoice:distance:distance.doc
|
||||
argchoice:dnaboot:dnaboot.doc
|
||||
argchoice:dnacomp:dnacomp.doc
|
||||
argchoice:dnadist:dnadist.doc
|
||||
argchoice:dnainvar:dnainvar.doc
|
||||
argchoice:dnaml:dnaml.doc
|
||||
argchoice:dnamlk:dnamlk.doc
|
||||
argchoice:dnamove:dnamove.doc
|
||||
argchoice:dnapars:dnapars.doc
|
||||
argchoice:dnapenny:dnapenny.doc
|
||||
argchoice:dolboot:dolboot.doc
|
||||
argchoice:dollop:dollop.doc
|
||||
argchoice:dolmove:dolmove.doc
|
||||
argchoice:dolpenny:dolpenny.doc
|
||||
argchoice:draw:draw.doc
|
||||
argchoice:drawgram:drawgram.doc
|
||||
argchoice:drawtree:drawtree.doc
|
||||
argchoice:factor:factor.doc
|
||||
argchoice:fitch:fitch.doc
|
||||
argchoice:gendist:gendist.doc
|
||||
argchoice:kitsch:kitsch.doc
|
||||
argchoice:main:main.doc
|
||||
argchoice:mix:mix.doc
|
||||
argchoice:move:move.doc
|
||||
argchoice:neighbor:neighbor.doc
|
||||
argchoice:penny:penny.doc
|
||||
argchoice:protpars:protpars.doc
|
||||
argchoice:read.me.general:read.me.general.doc
|
||||
argchoice:restml:restml.doc
|
||||
argchoice:seqboot:seqboot.doc
|
||||
argchoice:sequence:sequence.doc
|
||||
|
||||
|
||||
|
||||
item:Phylip 3.5
|
||||
itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT /usr/bin/X11/xterm -e $PROGRAM;kedit outfile; treetool outtree; rm in1 )&
|
||||
item:Phylip 3.4
|
||||
itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT shelltool $PROGRAM;textedit outfile;rm in1 )&
|
||||
|
||||
arg:PROGRAM
|
||||
argtype:choice_list
|
||||
|
|
@ -666,81 +879,358 @@ arg:PREEDIT
|
|||
argtype:chooser
|
||||
arglabel:Edit input before running?
|
||||
argchoice:No:
|
||||
argchoice:Yes:kedit infile;
|
||||
argchoice:Yes:textedit infile;
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
inmask:
|
||||
insave:
|
||||
|
||||
|
||||
|
||||
item:Phylip DNA Distance methods
|
||||
itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e dnadist;mv -f outfile infile; cp infile $DNA; /usr/bin/X11/xterm -e neighbor; cp outtree intree; cp outfile $NEI; $PROGRAM kedit outfile; cp outtree $TREE; treetool outtree; /bin/rm -f in1 infile outfile intree outtree)&
|
||||
|
||||
arg:EXPLAIN
|
||||
argtype:text
|
||||
arglabel:To produce a bootstraped tree choose DNADIST+NEIGHOR+CONSENSE
|
||||
|
||||
item:Phylip Distance methods
|
||||
itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ; $PREEDIT shelltool dnadist;mv -f outfile infile;$PROGRAM textedit outfile;/bin/rm -f in1 infile outfile)&
|
||||
|
||||
arg:PROGRAM
|
||||
arglabel:Which method?
|
||||
argtype:chooser
|
||||
argchoice:DNADIST+NEIGHBOR:
|
||||
argchoice:DNADIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense;
|
||||
|
||||
arg:PROG
|
||||
arglabel:Run ?
|
||||
argtype:chooser
|
||||
argchoice:Run without Bootstrap:
|
||||
argchoice:Run with Bootstrap: /usr/bin/X11/xterm -e seqboot;
|
||||
|
||||
arg:DNA
|
||||
argtype:text
|
||||
arglabel:Name of DNADIST outfile?
|
||||
|
||||
arg:NEI
|
||||
argtype:text
|
||||
arglabel:Name of NEIGHBOR outfile?
|
||||
|
||||
arg:TREE
|
||||
argtype:text
|
||||
arglabel:Name of TREEFILE ?
|
||||
argchoice:DNADIST:mv -f infile outfile;
|
||||
argchoice:Fitch:shelltool fitch;
|
||||
argchoice:Kitsch:shelltool kitsch;
|
||||
argchoice:Neighbor:shelltool neighbor;
|
||||
|
||||
arg:PREEDIT
|
||||
argtype:chooser
|
||||
arglabel:Edit input before running?
|
||||
argchoice:No:
|
||||
argchoice:Yes:kedit infile;
|
||||
argchoice:Yes:textedit infile;
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
inmask:
|
||||
insave:
|
||||
|
||||
item:Phylip PROTEIN Distance methods
|
||||
itemmethod:(readseq -a -f12 in1 > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e protdist;mv -f outfile infile; /usr/bin/X11/xterm -e neighbor; cp outtree intree; $PROGRAM kedit outfile;treetool outtree;/bin/rm -f in1 infile outfile)&
|
||||
menu:Email
|
||||
|
||||
arg:PROGRAM
|
||||
arglabel:Which method?
|
||||
argtype:chooser
|
||||
argchoice:PROTDIST+NEIGHBOR:
|
||||
argchoice:PROTDIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense;
|
||||
item:BLASTN
|
||||
itemmethod:(echo BLASTPROGRAM blastn > in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo MATCH $MSCORE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) &
|
||||
|
||||
arg:PROG
|
||||
arglabel:Which method?
|
||||
argtype:chooser
|
||||
argchoice:Bootstrap: /usr/bin/X11/xterm -e seqboot;
|
||||
argchoice:No Bootstrap:
|
||||
arg:DBASE
|
||||
argtype:choice_list
|
||||
arglabel:Which Database?
|
||||
argchoice:GenBank Qtrly & Updates:GenBank
|
||||
argchoice:EMBL:embl
|
||||
|
||||
arg:PREEDIT
|
||||
arg:MSCORE
|
||||
argtype:slider
|
||||
arglabel:Match Score
|
||||
argmin:3
|
||||
argmax:7
|
||||
argvalue:5
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
item:BLASTP
|
||||
itemmethod:(echo BLASTPROGRAM blastp >in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) &
|
||||
|
||||
arg:DBASE
|
||||
argtype:choice_list
|
||||
arglabel:Which Database?
|
||||
argchoice:Swiss-Prot:swiss-prot
|
||||
argchoice:PIR:pir
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
item:Fasta-(DNA)
|
||||
itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $KPL >> in1.tmp; echo SCORES $TOP >> in1.tmp; echo ALIGNMENTS $ALNG >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp;Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) &
|
||||
|
||||
arg:DBASE
|
||||
argtype:choice_list
|
||||
arglabel:Which GenBank Database?
|
||||
argchoice:Qrtly & Updates:GenBank/all
|
||||
argchoice:Updates:GenBank/new
|
||||
argchoice:Primate:GenBank/primate
|
||||
argchoice:Rodent:GenBank/rodent
|
||||
argchoice:Other-Mammalian:GenBank/other_mammalian
|
||||
argchoice:Other-Vertebrate:GenBank/other_vertebrate
|
||||
argchoice:Invertebrate:GenBank/invertebrate
|
||||
argchoice:Plant:GenBank/plant
|
||||
argchoice:Organelle:GenBank/organelle
|
||||
argchoice:Bacterial:GenBank/bacterial
|
||||
argchoice:Structural-RNA:GenBank/structural_rna
|
||||
argchoice:Viral:GenBank/viral
|
||||
argchoice:Phage:GenBank/phage
|
||||
argchoice:Synthetic:GenBank/synthetic
|
||||
argchoice:Unannotated:GenBank/unannotated
|
||||
|
||||
arg:KPL
|
||||
argtype:slider
|
||||
arglabel:K-tuple window
|
||||
argmin:3
|
||||
argmax:6
|
||||
argvalue:4
|
||||
|
||||
arg:TOP
|
||||
argtype:slider
|
||||
arglabel:Scores Displayed?
|
||||
argmin:1
|
||||
argmax:200
|
||||
argvalue:100
|
||||
|
||||
arg:ALNG
|
||||
argtype:slider
|
||||
arglabel:# Alignments Displayed?
|
||||
argmin:1
|
||||
argmax:200
|
||||
argvalue:20
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
item:Fasta-(PROTEIN)
|
||||
itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $TPL >> in1.tmp; echo SCORES $SCRS >> in1.tmp; echo ALIGNMENTS $ALNMNTS >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#$' '>' >> in1.tmp; Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) &
|
||||
|
||||
arg:DBASE
|
||||
argtype:choice_list
|
||||
arglabel:Which Protein Database?
|
||||
argchoice:Trans GenBank Qrtly:GenPept/all
|
||||
argchoice:Trans GenBank Daily:GenPept/new
|
||||
argchoice:Swiss-Protein:SWISS-PROT/all
|
||||
|
||||
arg:TPL
|
||||
argtype:slider
|
||||
arglabel:K-TUP window
|
||||
argmin:1
|
||||
argmax:2
|
||||
argvalue:1
|
||||
|
||||
arg:SCRS
|
||||
argtype:slider
|
||||
arglabel:# Scores Displayed?
|
||||
argmin:1
|
||||
argmax:200
|
||||
argvalue:100
|
||||
|
||||
arg:ALNMNTS
|
||||
argtype:slider
|
||||
arglabel:# Alignments Displayed?
|
||||
argmin:1
|
||||
argmax:200
|
||||
argvalue:20
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
item:GeneID
|
||||
itemmethod:($REPRINT > in1.tmp; echo Genomic Sequence >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail geneid@darwin.bu.edu < in1.tmp; rm in1 in1.tmp) &
|
||||
|
||||
arg:REPRINT
|
||||
argtype:chooser
|
||||
arglabel:Edit input before running?
|
||||
arglabel:Do you want a GENEID reprint?
|
||||
argchoice:YES:echo "Preprint Request" >> in1.tmp
|
||||
argchoice:NO
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
item:Sequence Retrieval
|
||||
itemmethod:(echo $REGEXP > in1.tmp; Mail RETRIEVE@GENBANK.BIO.NET < in1.tmp; rm in1.tmp) &
|
||||
|
||||
arg:REGEXP
|
||||
argtype:text
|
||||
arglabel:Accession # or LOCUS name of sequence to retrieve
|
||||
|
||||
item:Grail
|
||||
itemmethod:(echo Sequences $TOTALSEQS $ID > in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail grail@ornl.gov <in1.tmp; rm in1 in1.tmp) &
|
||||
|
||||
arg:REGISTER
|
||||
argtype:chooser
|
||||
arglabel:Have you previously registered for Grail services?
|
||||
argchoice:YES
|
||||
argchoice:NO:echo "YOU MUST REGISTER"
|
||||
|
||||
arg:TOTALSEQS
|
||||
argtype:text
|
||||
arglabel:Number of Sequences Being Sent to Grail?
|
||||
|
||||
arg:ID
|
||||
argtype:text
|
||||
arglabel:User ID (MUST HAVE PREVIOUSLY REGISTERED)
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
item:Grail Registration
|
||||
itemmethod:(echo Register > in1.tmp; echo $NAME >> in1.tmp; echo $ADDRESS >> in1.tmp; echo $PHONE >> in1.tmp; echo $EMAIL >> in1.tmp; Mail grail@ornl.gov < in1.tmp; rm in1.tmp)
|
||||
|
||||
arg:NAME
|
||||
argtype:text
|
||||
arglabel:Your Name
|
||||
|
||||
arg:ADDRESS
|
||||
argtype:text
|
||||
arglabel:Your Address
|
||||
|
||||
arg:PHONE
|
||||
argtype:text
|
||||
arglabel:Your Phone Number
|
||||
|
||||
arg:EMAIL
|
||||
argtype:text
|
||||
arglabel:Your E-Mail Address
|
||||
|
||||
|
||||
#
|
||||
# dgg added new readseq formats, 29 dec 92
|
||||
#
|
||||
|
||||
item:Export Foreign Format
|
||||
itemmethod:readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE
|
||||
itemhelp:readseq.help
|
||||
|
||||
arg:FORMAT
|
||||
argtype:choice_list
|
||||
argchoice:GenBank:genbank
|
||||
argchoice:IG/Stanford:ig
|
||||
argchoice:NBRF:nbrf
|
||||
argchoice:EMBL:embl
|
||||
argchoice:GCG:gcg
|
||||
argchoice:DNA Strider:strider
|
||||
argchoice:Fitch:fitch
|
||||
argchoice:Pearson/Fasta:pearson
|
||||
argchoice:Zuker:zuker
|
||||
argchoice:Olsen:olsen
|
||||
argchoice:Phylip:phylip
|
||||
#argchoice:Phylip v3.2:phylip3.2
|
||||
argchoice:Plain text:raw
|
||||
argchoice:ASN.1:asn
|
||||
argchoice:PIR:pir
|
||||
argchoice:MSF:msf
|
||||
argchoice:PAUP:paup
|
||||
argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop
|
||||
|
||||
arg:OUTPUTFILE
|
||||
argtype:text
|
||||
arglabel:Save as?
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
|
||||
|
||||
#
|
||||
#dgg addition for new readseq, 24 dec 92
|
||||
#
|
||||
|
||||
item:Pretty Print
|
||||
itemmethod:readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (textedit in1.pretty; /bin/rm -f in1 in1.pretty)&
|
||||
itemhelp:readseq.help
|
||||
|
||||
#nametop is bad !?
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
|
||||
arg:NAMETOP
|
||||
argtype:chooser
|
||||
arglabel:Names at top ?
|
||||
argchoice:No:
|
||||
argchoice:Yes:kedit infile;
|
||||
argchoice:Yes:-nametop
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
inmask:
|
||||
insave:
|
||||
arg:NAMELEFT
|
||||
argtype:chooser
|
||||
arglabel:Names at left ?
|
||||
argchoice:No:
|
||||
argchoice:Yes:-nameleft
|
||||
|
||||
arg:NAMERIGHT
|
||||
argtype:chooser
|
||||
arglabel:Names at right?
|
||||
argchoice:Yes:-nameright
|
||||
argchoice:No:
|
||||
|
||||
arg:NUMTOP
|
||||
argtype:chooser
|
||||
arglabel:Numbers at top ?
|
||||
argchoice:Yes:-numtop
|
||||
argchoice:No:
|
||||
|
||||
arg:NUMBOT
|
||||
argtype:chooser
|
||||
arglabel:Numbers at tail ?
|
||||
argchoice:No:
|
||||
argchoice:Yes:-numbot
|
||||
|
||||
arg:NUMLEFT
|
||||
argtype:chooser
|
||||
arglabel:Numbers at left ?
|
||||
argchoice:Yes:-numleft
|
||||
argchoice:No:
|
||||
|
||||
arg:NUMRIGHT
|
||||
argtype:chooser
|
||||
arglabel:Numbers at right?
|
||||
argchoice:Yes:-numright
|
||||
argchoice:No:
|
||||
|
||||
arg:MATCH
|
||||
argtype:chooser
|
||||
arglabel:Use match '.' for 2..n species?
|
||||
argchoice:No:
|
||||
argchoice:Yes:-match
|
||||
|
||||
arg:GAPC
|
||||
argtype:chooser
|
||||
arglabel:Count gap symbols?
|
||||
argchoice:No:
|
||||
argchoice:Yes:-gap
|
||||
|
||||
arg:WIDTH
|
||||
argtype:slider
|
||||
arglabel:Sequence width?
|
||||
argmin:10
|
||||
argmax:200
|
||||
argvalue:50
|
||||
|
||||
arg:COLS
|
||||
argtype:slider
|
||||
arglabel:Column spacers?
|
||||
argmin:0
|
||||
argmax:50
|
||||
argvalue:10
|
||||
|
||||
|
||||
### pretty print insert end
|
||||
#
|
||||
|
||||
item:Wally's test function
|
||||
itemmethod:run__wally $ONE $TWO $THREE < $FILE
|
||||
|
||||
arg:ONE
|
||||
argtype:chooser
|
||||
arglabel:How?
|
||||
argchoice:Fast:-fast
|
||||
argchoice:Slow:-slow
|
||||
|
||||
arg:TWO
|
||||
argtype:slider
|
||||
argmin:0
|
||||
argmax:100
|
||||
argvalue:50
|
||||
arglabel:how many?
|
||||
|
||||
arg:THREE
|
||||
argtype:choice_list
|
||||
arglabel:Which one?
|
||||
argchoice:Fast:-fast
|
||||
argchoice:Slow:-slow
|
||||
|
||||
arg:FILE
|
||||
argtype:text
|
||||
arglabel:Which file
|
||||
|
||||
|
|
|
|||
746
CORE/.GDEmenus.linux
Normal file
746
CORE/.GDEmenus.linux
Normal file
|
|
@ -0,0 +1,746 @@
|
|||
1menu:File
|
||||
|
||||
item:test cmask output
|
||||
itemmethod: kedit in1
|
||||
|
||||
in:in1
|
||||
informat:colormask
|
||||
|
||||
item:New sequence <meta N>
|
||||
itemmethod:echo "$Type$Name" > out1
|
||||
itemmeta:n
|
||||
itemhelp:new_sequence.help
|
||||
|
||||
arg:Name
|
||||
argtype:text
|
||||
arglabel:New Sequence name?
|
||||
argtext:New
|
||||
|
||||
arg:Type
|
||||
argtype:choice_list
|
||||
arglabel:Type?
|
||||
argchoice:DNA/RNA:#
|
||||
argchoice:Amino Acid:%
|
||||
argchoice:Text:\"
|
||||
argchoice:Mask:@
|
||||
|
||||
out:out1
|
||||
outformat:flat
|
||||
|
||||
item:Import Foreign Format
|
||||
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
|
||||
itemhelp:readseq.help
|
||||
|
||||
arg:INPUTFILE
|
||||
argtype:text
|
||||
arglabel:Name of foreign file?
|
||||
|
||||
out:OUTPUTFILE
|
||||
outformat:genbank
|
||||
|
||||
item:Export Foreign Format
|
||||
itemmethod:readseq INPUTFILE -a -f$FORMAT > $OUTPUTFILE
|
||||
itemhelp:readseq.help
|
||||
|
||||
arg:FORMAT
|
||||
argtype:choice_list
|
||||
argchoice:FASTA:8
|
||||
argchoice:NEXUS:17
|
||||
argchoice:Phylip v3.3:12
|
||||
argchoice:IG/Stanford:1
|
||||
argchoice:GenBank:2
|
||||
argchoice:NBRF:3
|
||||
argchoice:EMBL:4
|
||||
argchoice:GCG:5
|
||||
argchoice:DNA Strider:6
|
||||
argchoice:Fitch:7
|
||||
argchoice:Pearson:8
|
||||
argchoice:Zuker:9
|
||||
argchoice:Olsen:10
|
||||
argchoice:Phylip v3.2:11
|
||||
argchoice:Phylip v3.3:12
|
||||
argchoice:Plain text:13
|
||||
|
||||
arg:OUTPUTFILE
|
||||
argtype:text
|
||||
arglabel:Save as?
|
||||
|
||||
in:INPUTFILE
|
||||
informat:genbank
|
||||
|
||||
|
||||
item:Save Selection
|
||||
itemmethod: cat $SAVE_FUNC > $Name
|
||||
itemhelp:save_selection.help
|
||||
|
||||
arg:SAVE_FUNC
|
||||
argtype:chooser
|
||||
arglabel:File format
|
||||
argchoice:Flat:in1
|
||||
argchoice:Genbank:in2
|
||||
argchoice:GDE/HGL:in3
|
||||
|
||||
arg:Name
|
||||
argtype:text
|
||||
arglabel:File name?
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
|
||||
in:in2
|
||||
informat:genbank
|
||||
|
||||
in:in3
|
||||
informat:gde
|
||||
|
||||
item:Print Selection
|
||||
itemmethod:(PrintStrat in1 $SCALE > in1.tmp; $CMD -P$PRINTER in1.tmp; /bin/rm -f in1 in1.tmp)&
|
||||
itemhelp:print_alignment.help
|
||||
|
||||
arg:SCALE
|
||||
argtype:slider
|
||||
arglabel:Reduce printout by?
|
||||
argmin:1
|
||||
argmax:20
|
||||
argvalue:1
|
||||
|
||||
arg:CMD
|
||||
argtype:chooser
|
||||
argchoice:Lpr:lpr
|
||||
argchoice:Enscript Gaudy:enscript -G -q
|
||||
argchoice:Enscript Two column:enscript -2rG
|
||||
|
||||
arg:PRINTER
|
||||
argtype:text
|
||||
arglabel:Which printer?
|
||||
argtext:lp
|
||||
|
||||
in:in1
|
||||
informat:gde
|
||||
insave:
|
||||
|
||||
menu:Edit
|
||||
|
||||
item:Sort
|
||||
itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;/bin/rm -f in1*)&
|
||||
itemhelp:heapsortHGL.help
|
||||
|
||||
arg:PRIM_KEY
|
||||
argtype:choice_list
|
||||
argchoice:Group:group-ID
|
||||
argchoice:type:type
|
||||
argchoice:name:name
|
||||
argchoice:Sequence ID:sequence-ID
|
||||
argchoice:creator:creator
|
||||
argchoice:offset:offset
|
||||
arglabel:Primary sort field?
|
||||
|
||||
arg:SEC_KEY
|
||||
argtype:choice_list
|
||||
argchoice:None:
|
||||
argchoice:Group:group-ID
|
||||
argchoice:type:type
|
||||
argchoice:name:name
|
||||
argchoice:Sequence ID:sequence-ID
|
||||
argchoice:creator:creator
|
||||
argchoice:offset:offset
|
||||
arglabel:Secondary sort field?
|
||||
|
||||
in:in1
|
||||
informat:gde
|
||||
insave:
|
||||
|
||||
item:extract
|
||||
itemmethod:(gde in1;/bin/rm -f in1)&
|
||||
|
||||
in:in1
|
||||
informat:gde
|
||||
inmask:
|
||||
insave:
|
||||
|
||||
menu:DNA/RNA
|
||||
|
||||
item:Translate...
|
||||
itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE in1 > out1
|
||||
|
||||
arg:FRAME
|
||||
argtype:chooser
|
||||
arglabel:Which reading frame?
|
||||
argchoice:First:1
|
||||
argchoice:Second:2
|
||||
argchoice:Third:3
|
||||
argchoice:All six:6
|
||||
|
||||
arg:MNFRM
|
||||
arglabel:Minimum length of AA sequence to translate?
|
||||
argtype:slider
|
||||
argmin:0
|
||||
argmax:100
|
||||
argvalue:20
|
||||
|
||||
arg:LTRCODE
|
||||
argtype:chooser
|
||||
arglabel:Translate to:
|
||||
argchoice:Single letter codes:
|
||||
argchoice:Triple letter codes:-3
|
||||
|
||||
arg:TBL
|
||||
arglabel:Codon table?
|
||||
argtype:chooser
|
||||
argchoice:universal:1
|
||||
argchoice:mycoplasma:2
|
||||
argchoice:yeast:3
|
||||
argchoice:Vert. mito.:4
|
||||
in:in1
|
||||
informat:gde
|
||||
|
||||
out:out1
|
||||
outformat:gde
|
||||
|
||||
item:Dot plot
|
||||
itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)&
|
||||
itemhelp:DotPlotTool.help
|
||||
|
||||
in:in1
|
||||
informat:gde
|
||||
insave:
|
||||
|
||||
item:Clustal alignment
|
||||
itemmethod:(tr '%#' '>'<in1>clus_in;clustalw -quicktree -output=PIR -infile=clus_in -align > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1;/bin/rm -f clus_in* in1* )&
|
||||
|
||||
itemhelp:clustal_help
|
||||
|
||||
arg:KTUP
|
||||
argtype:slider
|
||||
arglabel:K-tuple size for pairwise search
|
||||
argmin:1
|
||||
argmax:10
|
||||
argvalue:2
|
||||
|
||||
arg:WIN
|
||||
argtype:slider
|
||||
arglabel:Window size
|
||||
argmin:1
|
||||
argmax:10
|
||||
argvalue:4
|
||||
|
||||
arg:Trans
|
||||
argtype:chooser
|
||||
arglabel:Transitions weighted?
|
||||
argchoice:Yes:/TRANSIT
|
||||
argchoice:No:
|
||||
|
||||
arg:FIXED
|
||||
argtype:slider
|
||||
arglabel:Fixed gap penalty
|
||||
argmin:1
|
||||
argmax:100
|
||||
argvalue:10
|
||||
|
||||
arg:FLOAT
|
||||
arglabel:Floating gap penalty
|
||||
argtype:slider
|
||||
argmin:1
|
||||
argmax:100
|
||||
argvalue:10
|
||||
|
||||
arg:REPORT
|
||||
argtype:chooser
|
||||
arglabel:View assembly report?
|
||||
argchoice:No:
|
||||
argchoice:Yes:kedit in1.rpt&
|
||||
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
item:Variable Positions
|
||||
itemmethod:varpos $REV < in1 > out1
|
||||
|
||||
arg:REV
|
||||
argtype:chooser
|
||||
arglabel:Highlight (darken)
|
||||
argchoice:Conserved positions:
|
||||
argchoice:variable positions:-rev
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
|
||||
out:out1
|
||||
outformat:colormask
|
||||
|
||||
item:Phrap
|
||||
itemmethod:readseq in1 -a -f8 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp; phrap OUTPUTFILE; readseq -a -f2 OUTPUTFILE.contigs > out1;/bin/rm -rf OUTPUT*;
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
|
||||
out:out1
|
||||
outformat:genbank
|
||||
|
||||
item:SNAP
|
||||
itemmethod: cat in1 > infile;/usr/local/bio/GDE/bin/fasta2snap.pl > outfile; /usr/bin/X11/xterm -e /home/tulio/bio/SNAP/SNAP.pl outfile; kedit backg*; kedit summ*; sheeltool /home/tulio/bio/codons-xyplot.pl codons.*; kedit codon.data; /bin/rm -rf back* codon* summ*;
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
out:out1
|
||||
outformat:text
|
||||
|
||||
|
||||
|
||||
|
||||
item:Find all <meta-f>
|
||||
itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1;
|
||||
itemhelp:findall.help
|
||||
itemmeta:f
|
||||
|
||||
arg:SEARCH
|
||||
argtype:text
|
||||
arglabel:Search String
|
||||
|
||||
arg:PRCNT
|
||||
argtype:slider
|
||||
arglabel:Percent mismatch
|
||||
argmin:0
|
||||
argmax:75
|
||||
argvalue:10
|
||||
|
||||
arg:CASE
|
||||
argtype:chooser
|
||||
arglabel:Case
|
||||
argchoice:Upper equals lower:
|
||||
argchoice:Upper not equal lower:-case
|
||||
|
||||
arg:UT
|
||||
argtype:chooser
|
||||
arglabel:U equal T?
|
||||
argchoice:Yes:-u=t
|
||||
argchoice:No:
|
||||
argvalue:0
|
||||
|
||||
arg:MAT
|
||||
arglabel:Match color
|
||||
argtype:choice_list
|
||||
argchoice:yellow:1
|
||||
argchoice:violet:2
|
||||
argchoice:red:3
|
||||
argchoice:aqua:4
|
||||
argchoice:green:5
|
||||
argchoice:blue:6
|
||||
argchoice:grey:11
|
||||
argchoice:black:8
|
||||
argvalue:2
|
||||
|
||||
arg:MIS
|
||||
argtype:choice_list
|
||||
arglabel:Mismatch color
|
||||
argchoice:yellow:1
|
||||
argchoice:violet:2
|
||||
argchoice:red:3
|
||||
argchoice:aqua:4
|
||||
argchoice:green:5
|
||||
argchoice:blue:6
|
||||
argchoice:grey:11
|
||||
argchoice:black:8
|
||||
argvalue:7
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
|
||||
out:out1
|
||||
outformat:colormask
|
||||
|
||||
item:Sequence Consensus
|
||||
itemmethod:(MakeCons in1 $METHOD $MASK > out1)
|
||||
itemhelp:MakeCons.help
|
||||
|
||||
arg:METHOD
|
||||
arglabel:Method
|
||||
argtype:chooser
|
||||
argchoice:IUPAC:-iupac
|
||||
argchoice:Majority:-majority $PERCENT
|
||||
|
||||
arg:MASK
|
||||
argtype:chooser
|
||||
arglabel:Create a new:
|
||||
argchoice:Sequence:
|
||||
argchoice:Selection Mask: | Consto01mask
|
||||
|
||||
arg:PERCENT
|
||||
arglabel:Minimum Percentage for Majority
|
||||
argtype:slider
|
||||
argmin:50
|
||||
argmax:100
|
||||
argvalue:75
|
||||
|
||||
in:in1
|
||||
informat:gde
|
||||
|
||||
out:out1
|
||||
outformat:gde
|
||||
|
||||
|
||||
#Menu for DNA/RNA
|
||||
|
||||
item:blastn
|
||||
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; /usr/local/bio/blast/blastall -p blastn -d $BLASTDBDNA -i in1.f -W $WORDLEN -M $MATCH > in1.tmp; kedit in1.tmp; rm in1*)&
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
arg:BLASTDBDNA
|
||||
argtype:choice_list
|
||||
arglabel:Which Database
|
||||
argchoice:HIV-1 Seq. Db.:/usr/local/bio/db/DNA/hiv17-08-01.fasta2
|
||||
arg:WORDLEN
|
||||
argtype:slider
|
||||
arglabel:Word Size
|
||||
argmin:4
|
||||
argmax:18
|
||||
argvalue:12
|
||||
|
||||
arg:MATCH
|
||||
argtype:slider
|
||||
arglabel:Match Score
|
||||
argmin:1
|
||||
argmax:10
|
||||
argvalue:5
|
||||
|
||||
arg:MMSCORE
|
||||
argtype:slider
|
||||
arglabel:Mismatch Score
|
||||
argmin:-10
|
||||
argmax:-1
|
||||
argvalue:-5
|
||||
|
||||
item:blastx
|
||||
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; /usr/local/bio/blast/blastall -p blastx -d $BLASTDB -i in1.f -W $WORDLEN -M PAM30 > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1*)&
|
||||
|
||||
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
arg:BLASTDBDNA
|
||||
argtype:choice_list
|
||||
arglabel:Which Database
|
||||
argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta
|
||||
argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
|
||||
|
||||
arg:WORDLEN
|
||||
argtype:slider
|
||||
arglabel:Word Size
|
||||
argmin:1
|
||||
argmax:5
|
||||
argvalue:3
|
||||
|
||||
arg:Matrix
|
||||
arglabel:Substitution Matrix:
|
||||
argtype:choice_list
|
||||
argchoice:PAM30:PAM30
|
||||
argchoice:PAM70:PAM70
|
||||
|
||||
arg:CODE
|
||||
argtype:choice_list
|
||||
arglabel:Genetic Code
|
||||
|
||||
argchoice:Standard or Universal:0
|
||||
argchoice:Vertebrate Mitochondrial:1
|
||||
argchoice:Yeast Mitochondrial:2
|
||||
argchoice:Mold Mitochondrial and Mycoplasma:3
|
||||
argchoice:Invertebrate Mitochondrial:4
|
||||
argchoice:Ciliate Macronuclear:5
|
||||
argchoice:Protozoan Mitochondrial:6
|
||||
argchoice:Plant Mitochondrial:7
|
||||
argchoice:Echinodermate Mitochondrial:8
|
||||
|
||||
item:------------------------
|
||||
|
||||
item:Add a new DNA blast db
|
||||
itemmethod:xterm -e formatdb -i $sourcefile -p F -o T; /usr/local/bio/GDE/bin/installBLASTDB.pl $sourcefile $menuname;
|
||||
|
||||
arg:sourcefile
|
||||
argtype:text
|
||||
arglabel: enter the file name
|
||||
|
||||
arg:menuname
|
||||
argtype:text
|
||||
arglabel: enter the name of the DB
|
||||
|
||||
|
||||
#Sequence dataset
|
||||
menu:seq. datasets
|
||||
|
||||
|
||||
item:-------------
|
||||
item:add a new dataset
|
||||
itemmethod:mkdir db; cp $file db/ ;xterm -e /usr/local/bio/GDE/newDATASET.pl $name $file
|
||||
|
||||
arg:name
|
||||
argtype:text
|
||||
arglabel:Enter the dataset name ?
|
||||
|
||||
arg:file
|
||||
argtype:text
|
||||
arglabel:Enter the dataset file (in FASTA) ?
|
||||
|
||||
|
||||
#Menu for Protein
|
||||
menu:protein
|
||||
item:blastp
|
||||
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp /usr/local/bio/db/PAM30; /usr/local/bio/blast/blastall -p blastp -d $BLASTDBPROT -i in1.f -W $WORDLEN -M $Matrix > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1* PAM30)&
|
||||
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
arg:BLASTDBPROT
|
||||
argtype:choice_list
|
||||
arglabel:Which Database
|
||||
argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta
|
||||
|
||||
arg:Matrix
|
||||
barglabel:Substitution Matrix:
|
||||
argtype:choice_list
|
||||
argchoice:PAM30:PAM30
|
||||
argchoice:PAM70:PAM70
|
||||
|
||||
arg:WORDLEN
|
||||
argtype:slider
|
||||
arglabel:Word Size
|
||||
argmin:1
|
||||
argmax:5
|
||||
argvalue:3
|
||||
|
||||
item:tblastn
|
||||
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp /usr/local/bio/db/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; kedit in1.tmp; rm in1* PAM???)&
|
||||
|
||||
in:in1
|
||||
informat:flat
|
||||
insave:
|
||||
|
||||
arg:BLASTDB
|
||||
argtype:choice_list
|
||||
arglabel:Which Database
|
||||
argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank
|
||||
argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate
|
||||
|
||||
arg:Matrix
|
||||
arglabel:Substitution Matrix:
|
||||
argtype:choice_list
|
||||
argchoice:PAM30:PAM30
|
||||
argchoice:PAM70:PAM70
|
||||
|
||||
arg:WORDLEN
|
||||
argtype:slider
|
||||
arglabel:Word Size
|
||||
argmin:4
|
||||
argmax:18
|
||||
argvalue:12
|
||||
|
||||
arg:CODE
|
||||
argtype:choice_list
|
||||
arglabel:Genetic Code
|
||||
argchoice:Standard or Universal:0
|
||||
argchoice:Vertebrate Mitochondrial:1
|
||||
argchoice:Yeast Mitochondrial:2
|
||||
argchoice:Mold Mitochondrial and Mycoplasma:3
|
||||
argchoice:Invertebrate Mitochondrial:4
|
||||
argchoice:Ciliate Macronuclear:5
|
||||
argchoice:Protozoan Mitochondrial:6
|
||||
argchoice:Plant Mitochondrial:7
|
||||
argchoice:Echinodermate Mitochondrial:8
|
||||
|
||||
|
||||
item:Map View
|
||||
itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)&
|
||||
itemhelp:mapview.help
|
||||
|
||||
in:in1
|
||||
informat:gde
|
||||
insave:
|
||||
|
||||
arg:PBL
|
||||
arglabel:Pixel Between Lines
|
||||
argtype:slider
|
||||
argvalue:10
|
||||
argmin:1
|
||||
argmax:15
|
||||
|
||||
arg:NPP
|
||||
arglabel:Nucleotides Per Pixel
|
||||
argtype:slider
|
||||
argvalue:1
|
||||
argmin:1
|
||||
argmax:20
|
||||
|
||||
arg:LWIDTH
|
||||
arglabel:Line Thickness
|
||||
argtype:slider
|
||||
argvalue:2
|
||||
argmin:1
|
||||
argmax:5
|
||||
|
||||
item:--------------------------
|
||||
item:Add a new Protein blast db
|
||||
itemmethod:xterm -e formatdb -i $sourcefile -p T -o T; /usr/local/bio/GDE/bin/installBLASTDBPROT.pl $sourcefile $menuname;
|
||||
|
||||
arg:sourcefile
|
||||
argtype:text
|
||||
arglabel: Enter the file (in FASTA)
|
||||
|
||||
arg:menuname
|
||||
argtype:text
|
||||
arglabel: Enter the name of the DB
|
||||
|
||||
#Phylogenetic Menu
|
||||
|
||||
menu:Phylogeny
|
||||
|
||||
item:Phylip help
|
||||
itemmethod:(netscape /usr/local/bio/phylip/doc/$FILE)&
|
||||
|
||||
arg:FILE
|
||||
argtype:choice_list
|
||||
arglabel:Which program?
|
||||
argchoice:clique:clique.html
|
||||
argchoice:consense:consense.html
|
||||
argchoice:contchar:contchar.html
|
||||
argchoice:contml:contml.html
|
||||
argchoice:contrast:contrast.html
|
||||
argchoice:discrete:discrete.html
|
||||
argchoice:distance:distance.html
|
||||
argchoice:dnaboot:dnaboot.html
|
||||
argchoice:dnacomp:dnacomp.html
|
||||
argchoice:dnadist:dnadist.html
|
||||
argchoice:dnainvar:dnainvar.html
|
||||
argchoice:dnaml:dnaml.html
|
||||
argchoice:dnamlk:dnamlk.html
|
||||
argchoice:dnamove:dnamove.html
|
||||
argchoice:dnapars:dnapars.html
|
||||
argchoice:dnapenny:dnapenny.html
|
||||
argchoice:dollop:dollop.html
|
||||
argchoice:dolmove:dolmove.html
|
||||
argchoice:dolpenny:dolpenny.html
|
||||
argchoice:draw:draw.html
|
||||
argchoice:drawgram:drawgram.html
|
||||
argchoice:drawtree:drawtree.html
|
||||
argchoice:factor:factor.html
|
||||
argchoice:fitch:fitch.html
|
||||
argchoice:gendist:gendist.html
|
||||
argchoice:kitsch:kitsch.html
|
||||
argchoice:main:main.html
|
||||
argchoice:mix:mix.html
|
||||
argchoice:move:move.html
|
||||
argchoice:neighbor:neighbor.html
|
||||
argchoice:penny:penny.html
|
||||
argchoice:protpars:protpars.html
|
||||
argchoice:read.me.general:read.me.general.html
|
||||
argchoice:restml:restml.html
|
||||
argchoice:seqboot:seqboot.html
|
||||
argchoice:sequence:sequence.html
|
||||
|
||||
|
||||
|
||||
item:Phylip 3.5
|
||||
itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT /usr/bin/X11/xterm -e $PROGRAM;kedit outfile; treetool outtree; rm in1 )&
|
||||
|
||||
arg:PROGRAM
|
||||
argtype:choice_list
|
||||
arglabel:Which program to run?
|
||||
argchoice:DNAPARS:dnapars
|
||||
argchoice:DNABOOT:dnaboot
|
||||
argchoice:DNAPENNY:dnapenny
|
||||
argchoice:DNAML:dnaml
|
||||
argchoice:DNAMLK:dnamlk
|
||||
argchoice:DNACOMP:dnacomp
|
||||
argchoice:DNAMOVE:dnamove
|
||||
argchoice:DNAINVAR:dnainvar
|
||||
argchoice:PROTPARS:protpars
|
||||
|
||||
arg:PREEDIT
|
||||
argtype:chooser
|
||||
arglabel:Edit input before running?
|
||||
argchoice:No:
|
||||
argchoice:Yes:kedit infile;
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
inmask:
|
||||
insave:
|
||||
|
||||
|
||||
|
||||
item:Phylip DNA Distance methods
|
||||
itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e dnadist;mv -f outfile infile; cp infile $DNA; /usr/bin/X11/xterm -e neighbor; cp outtree intree; cp outfile $NEI; $PROGRAM kedit outfile; cp outtree $TREE; treetool outtree; /bin/rm -f in1 infile outfile intree outtree)&
|
||||
|
||||
arg:EXPLAIN
|
||||
argtype:text
|
||||
arglabel:To produce a bootstraped tree choose DNADIST+NEIGHOR+CONSENSE
|
||||
|
||||
|
||||
arg:PROGRAM
|
||||
arglabel:Which method?
|
||||
argtype:chooser
|
||||
argchoice:DNADIST+NEIGHBOR:
|
||||
argchoice:DNADIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense;
|
||||
|
||||
arg:PROG
|
||||
arglabel:Run ?
|
||||
argtype:chooser
|
||||
argchoice:Run without Bootstrap:
|
||||
argchoice:Run with Bootstrap: /usr/bin/X11/xterm -e seqboot;
|
||||
|
||||
arg:DNA
|
||||
argtype:text
|
||||
arglabel:Name of DNADIST outfile?
|
||||
|
||||
arg:NEI
|
||||
argtype:text
|
||||
arglabel:Name of NEIGHBOR outfile?
|
||||
|
||||
arg:TREE
|
||||
argtype:text
|
||||
arglabel:Name of TREEFILE ?
|
||||
|
||||
arg:PREEDIT
|
||||
argtype:chooser
|
||||
arglabel:Edit input before running?
|
||||
argchoice:No:
|
||||
argchoice:Yes:kedit infile;
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
inmask:
|
||||
insave:
|
||||
|
||||
item:Phylip PROTEIN Distance methods
|
||||
itemmethod:(readseq -a -f12 in1 > infile ;$PROG mv -f outfile infile; /usr/bin/X11/xterm -e protdist;mv -f outfile infile; /usr/bin/X11/xterm -e neighbor; cp outtree intree; $PROGRAM kedit outfile;treetool outtree;/bin/rm -f in1 infile outfile)&
|
||||
|
||||
arg:PROGRAM
|
||||
arglabel:Which method?
|
||||
argtype:chooser
|
||||
argchoice:PROTDIST+NEIGHBOR:
|
||||
argchoice:PROTDIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense;
|
||||
|
||||
arg:PROG
|
||||
arglabel:Which method?
|
||||
argtype:chooser
|
||||
argchoice:Bootstrap: /usr/bin/X11/xterm -e seqboot;
|
||||
argchoice:No Bootstrap:
|
||||
|
||||
arg:PREEDIT
|
||||
argtype:chooser
|
||||
arglabel:Edit input before running?
|
||||
argchoice:No:
|
||||
argchoice:Yes:kedit infile;
|
||||
|
||||
in:in1
|
||||
informat:genbank
|
||||
inmask:
|
||||
insave:
|
||||
|
||||
1236
CORE/.GDEmenus.sunos
Normal file
1236
CORE/.GDEmenus.sunos
Normal file
File diff suppressed because it is too large
Load diff
Loading…
Reference in a new issue