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: #Online menu 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://)