1menu:File
item:test cmask output
itemmethod: kedit in1
in:in1
informat:colormask
item:New sequence
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 $LTRCODE in1 > out1
arg:FRAME
argtype:chooser
arglabel:Which reading frame?
argchoice:First:1
argchoice:Second:2
argchoice:Third:3
argchoice:All six:6
arg:MNFRM
arglabel:Minimum length of AA sequence to translate?
argtype:slider
argmin:0
argmax:100
argvalue:20
arg:LTRCODE
argtype:chooser
arglabel:Translate to:
argchoice:Single letter codes:
argchoice:Triple letter codes:-3
arg:TBL
arglabel:Codon table?
argtype:chooser
argchoice:universal:1
argchoice:mycoplasma:2
argchoice:yeast:3
argchoice:Vert. mito.:4
in:in1
informat:gde
out:out1
outformat:gde
item:Dot plot
itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)&
itemhelp:DotPlotTool.help
in:in1
informat:gde
insave:
item:Clustal alignment
itemmethod:(tr '%#' '>'clus_in;clustalw -quicktree -output=PIR -infile=clus_in -align > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$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
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.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.f; /usr/local/bio/blast/blastall -p blastx -d $BLASTDB -i in1.f -W $WORDLEN -M PAM30 > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1*)&
in:in1
informat:flat
insave:
arg:BLASTDB
argtype:choice_list
arglabel:Which Database
argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta
argchoice:genpept:$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/installBLASTDB.pl $sourcefile $menuname;
arg:sourcefile
argtype:text
arglabel: enter the file name
arg:menuname
argtype:text
arglabel: enter the name of the DB
menu:seq. datasets
item:-------------
item:add a new dataset
itemmethod:cp $file /usr/local/bio/GDE/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.f; cp /usr/local/bio/db/PAM30; /usr/local/bio/blast/blastall -p blastp -d $BLASTDB -i in1.f -W $WORDLEN -M $Matrix > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1* PAM30)&
in:in1
informat:flat
insave:
arg:BLASTDB
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.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 DNA blast db
itemmethod:xterm -e formatdb -i $sourcefile -p T -o T; /usr/local/bio/GDE/installBLASTDBPROT.pl $sourcefile $menuname;
arg:sourcefile
argtype:text
arglabel: Enter the file (in FASTA)
arg:menuname
argtype:text
arglabel: Enter the name of the DB
menu:Phylogeny
item:Phylip help
itemmethod:(netscape /usr/local/bio/phylip/doc/$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:
menu:On-Line Res.
item:GDE for Linux resources at Bioafrica.net
itemmethod:netscape http://www.bioafrica.net &
item:-------------------------
item:add a new website
itemmethod:xterm -e /usr/local/bio/GDE/newURL.pl $name $url
arg:name
argtype:text
arglabel:Enter the site name
arg:url
argtype:text
arglabel:Enter the URL (including http://)