762 lines
14 KiB
Plaintext
762 lines
14 KiB
Plaintext
1menu:File
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item:test cmask output
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itemmethod: kedit in1
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in:in1
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informat:colormask
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item:New sequence <meta N>
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itemmethod:echo "$Type$Name" > out1
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itemmeta:n
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itemhelp:new_sequence.help
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arg:Name
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argtype:text
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arglabel:New Sequence name?
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argtext:New
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arg:Type
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argtype:choice_list
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arglabel:Type?
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argchoice:DNA/RNA:#
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argchoice:Amino Acid:%
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argchoice:Text:\"
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argchoice:Mask:@
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out:out1
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outformat:flat
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item:Import Foreign Format
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itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
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itemhelp:readseq.help
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arg:INPUTFILE
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argtype:text
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arglabel:Name of foreign file?
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out:OUTPUTFILE
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outformat:genbank
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item:Export Foreign Format
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itemmethod:readseq INPUTFILE -a -f$FORMAT > $OUTPUTFILE
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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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argchoice:EMBL:4
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argchoice:GCG:5
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argchoice:DNA Strider:6
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argchoice:Fitch:7
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argchoice:Pearson:8
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argchoice:Zuker:9
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argchoice:Olsen:10
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argchoice:Phylip v3.2:11
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argchoice:Phylip v3.3:12
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argchoice:Plain text:13
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arg:OUTPUTFILE
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argtype:text
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arglabel:Save as?
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in:INPUTFILE
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informat:genbank
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item:Save Selection
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itemmethod: cat $SAVE_FUNC > $Name
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itemhelp:save_selection.help
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arg:SAVE_FUNC
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argtype:chooser
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arglabel:File format
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argchoice:Flat:in1
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argchoice:Genbank:in2
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argchoice:GDE/HGL:in3
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arg:Name
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argtype:text
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arglabel:File name?
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in:in1
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informat:flat
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in:in2
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informat:genbank
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in:in3
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informat:gde
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item:Print Selection
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itemmethod:(PrintStrat in1 $SCALE > in1.tmp; $CMD -P$PRINTER in1.tmp; /bin/rm -f in1 in1.tmp)&
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itemhelp:print_alignment.help
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arg:SCALE
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argtype:slider
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arglabel:Reduce printout by?
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argmin:1
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argmax:20
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argvalue:1
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arg:CMD
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argtype:chooser
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argchoice:Lpr:lpr
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argchoice:Enscript Gaudy:enscript -G -q
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argchoice:Enscript Two column:enscript -2rG
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arg:PRINTER
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argtype:text
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arglabel:Which printer?
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argtext:lp
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in:in1
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informat:gde
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insave:
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menu:Edit
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item:Sort
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itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;/bin/rm -f in1*)&
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itemhelp:heapsortHGL.help
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arg:PRIM_KEY
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argtype:choice_list
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argchoice:Group:group-ID
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argchoice:type:type
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argchoice:name:name
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argchoice:Sequence ID:sequence-ID
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argchoice:creator:creator
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argchoice:offset:offset
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arglabel:Primary sort field?
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arg:SEC_KEY
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argtype:choice_list
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argchoice:None:
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argchoice:Group:group-ID
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argchoice:type:type
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argchoice:name:name
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argchoice:Sequence ID:sequence-ID
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argchoice:creator:creator
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argchoice:offset:offset
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arglabel:Secondary sort field?
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in:in1
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informat:gde
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insave:
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item:extract
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itemmethod:(gde in1;/bin/rm -f in1)&
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in:in1
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informat:gde
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inmask:
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insave:
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menu:DNA/RNA
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item:Translate...
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itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE in1 > out1
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arg:FRAME
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argtype:chooser
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arglabel:Which reading frame?
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argchoice:First:1
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argchoice:Second:2
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argchoice:Third:3
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argchoice:All six:6
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arg:MNFRM
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arglabel:Minimum length of AA sequence to translate?
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argtype:slider
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argmin:0
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argmax:100
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argvalue:20
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arg:LTRCODE
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argtype:chooser
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arglabel:Translate to:
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argchoice:Single letter codes:
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argchoice:Triple letter codes:-3
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arg:TBL
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arglabel:Codon table?
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argtype:chooser
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argchoice:universal:1
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argchoice:mycoplasma:2
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argchoice:yeast:3
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argchoice:Vert. mito.:4
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in:in1
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informat:gde
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out:out1
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outformat:gde
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item:Dot plot
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itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)&
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itemhelp:DotPlotTool.help
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in:in1
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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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itemhelp:clustal_help
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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: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:Trans
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argtype:chooser
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arglabel:Transitions weighted?
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argchoice:Yes:/TRANSIT
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argchoice:No:
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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:kedit in1.rpt&
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in:in1
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informat:flat
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insave:
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item:Variable Positions
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itemmethod:varpos $REV < in1 > out1
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arg:REV
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argtype:chooser
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arglabel:Highlight (darken)
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argchoice:Conserved positions:
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argchoice:variable positions:-rev
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in:in1
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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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itemhelp:findall.help
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itemmeta:f
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arg:SEARCH
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argtype:text
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arglabel:Search String
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arg:PRCNT
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argtype:slider
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arglabel:Percent mismatch
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argmin:0
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argmax:75
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argvalue:10
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arg:CASE
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argtype:chooser
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arglabel:Case
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argchoice:Upper equals lower:
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argchoice:Upper not equal lower:-case
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arg:UT
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argtype:chooser
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arglabel:U equal T?
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argchoice:Yes:-u=t
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argchoice:No:
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argvalue:0
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arg:MAT
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arglabel:Match color
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argtype:choice_list
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argchoice:yellow:1
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argchoice:violet:2
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argchoice:red:3
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argchoice:aqua:4
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argchoice:green:5
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argchoice:blue:6
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argchoice:grey:11
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argchoice:black:8
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argvalue:2
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arg:MIS
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argtype:choice_list
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arglabel:Mismatch color
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argchoice:yellow:1
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argchoice:violet:2
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argchoice:red:3
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argchoice:aqua:4
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argchoice:green:5
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argchoice:blue:6
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argchoice:grey:11
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argchoice:black:8
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argvalue:7
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in:in1
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informat:flat
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out:out1
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outformat:colormask
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item:Sequence Consensus
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itemmethod:(MakeCons in1 $METHOD $MASK > out1)
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itemhelp:MakeCons.help
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arg:METHOD
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arglabel:Method
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argtype:chooser
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argchoice:IUPAC:-iupac
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argchoice:Majority:-majority $PERCENT
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arg:MASK
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argtype:chooser
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arglabel:Create a new:
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argchoice:Sequence:
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argchoice:Selection Mask: | Consto01mask
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arg:PERCENT
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arglabel:Minimum Percentage for Majority
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argtype:slider
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argmin:50
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argmax:100
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argvalue:75
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in:in1
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informat:gde
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out:out1
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outformat:gde
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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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in:in1
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informat:flat
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insave:
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arg:BLASTDBDNA
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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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arg:WORDLEN
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argtype:slider
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arglabel:Word Size
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argmin:4
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argmax:18
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argvalue:12
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arg:MATCH
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argtype:slider
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arglabel:Match Score
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argmin:1
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argmax:10
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argvalue:5
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arg:MMSCORE
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argtype:slider
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arglabel:Mismatch Score
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argmin:-10
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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 $WORDLEN -M PAM30 > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1*)&
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in:in1
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informat:flat
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insave:
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arg:BLASTDB
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argtype:choice_list
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arglabel:Which Database
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argchoice:HIV Proteins:/usr/local/bio/db/hiv17-08-01.PROT.fasta
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argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
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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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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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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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argchoice:Mold Mitochondrial and Mycoplasma:3
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argchoice:Invertebrate Mitochondrial:4
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argchoice:Ciliate Macronuclear:5
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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/installBLASTDB.pl $sourcefile $menuname;
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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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arg:menuname
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argtype:text
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arglabel: enter the name of the DB
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menu:seq. datasets
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item:-------------
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item:add a new dataset
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itemmethod:cp $file /usr/local/biotools/GDE/db/ ;xterm -e /usr/local/biotools/GDE/newDATASET.pl $name $file
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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:file
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argtype:text
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arglabel:Enter the dataset file (in FASTA) ?
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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 $BLASTDB -i in1.f -W $WORDLEN -M $Matrix > in1.tmp; /usr/openwin/bin/kedit in1.tmp; rm in1* PAM30)&
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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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arg:Matrix
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barglabel: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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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: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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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:genbank:$GDE_HELP_DIR/BLAST/genbank
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argchoice:genbank update:$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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arg:WORDLEN
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argtype:slider
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arglabel:Word Size
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argmin:4
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argmax:18
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argvalue:12
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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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argchoice:Mold Mitochondrial and Mycoplasma:3
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argchoice:Invertebrate Mitochondrial:4
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argchoice:Ciliate Macronuclear:5
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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:Map View
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itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)&
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itemhelp:mapview.help
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in:in1
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informat:gde
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insave:
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arg:PBL
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arglabel:Pixel Between Lines
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argtype:slider
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argvalue:10
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argmin:1
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argmax:15
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arg:NPP
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arglabel:Nucleotides Per Pixel
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argtype:slider
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argvalue:1
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argmin:1
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argmax:20
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arg:LWIDTH
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arglabel:Line Thickness
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argtype:slider
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argvalue:2
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argmin:1
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argmax:5
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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 T -o T; /usr/local/bio/GDE/installBLASTDBPROT.pl $sourcefile $menuname;
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arg:sourcefile
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argtype:text
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arglabel: Enter the file (in FASTA)
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arg:menuname
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argtype:text
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arglabel: Enter the name of the DB
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menu:Phylogeny
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item:Phylip help
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itemmethod:(netscape /usr/local/bio/phylip/doc/$FILE)&
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arg:FILE
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argtype:choice_list
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arglabel:Which program?
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argchoice:clique:clique.html
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argchoice:consense:consense.html
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argchoice:contchar:contchar.html
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argchoice:contml:contml.html
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argchoice:contrast:contrast.html
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argchoice:discrete:discrete.html
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argchoice:distance:distance.html
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argchoice:dnaboot:dnaboot.html
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argchoice:dnacomp:dnacomp.html
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argchoice:dnadist:dnadist.html
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argchoice:dnainvar:dnainvar.html
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argchoice:dnaml:dnaml.html
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argchoice:dnamlk:dnamlk.html
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argchoice:dnamove:dnamove.html
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argchoice:dnapars:dnapars.html
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argchoice:dnapenny:dnapenny.html
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argchoice:dollop:dollop.html
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argchoice:dolmove:dolmove.html
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argchoice:dolpenny:dolpenny.html
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argchoice:draw:draw.html
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argchoice:drawgram:drawgram.html
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argchoice:drawtree:drawtree.html
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argchoice:factor:factor.html
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argchoice:fitch:fitch.html
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argchoice:gendist:gendist.html
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argchoice:kitsch:kitsch.html
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argchoice:main:main.html
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argchoice:mix:mix.html
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argchoice:move:move.html
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argchoice:neighbor:neighbor.html
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argchoice:penny:penny.html
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argchoice:protpars:protpars.html
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argchoice:read.me.general:read.me.general.html
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argchoice:restml:restml.html
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argchoice:seqboot:seqboot.html
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argchoice:sequence:sequence.html
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item:Phylip 3.5
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itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT /usr/bin/X11/xterm -e $PROGRAM;kedit outfile; treetool outtree; rm in1 )&
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arg:PROGRAM
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argtype:choice_list
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arglabel:Which program to run?
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argchoice:DNAPARS:dnapars
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argchoice:DNABOOT:dnaboot
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argchoice:DNAPENNY:dnapenny
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argchoice:DNAML:dnaml
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argchoice:DNAMLK:dnamlk
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argchoice:DNACOMP:dnacomp
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argchoice:DNAMOVE:dnamove
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argchoice:DNAINVAR:dnainvar
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argchoice:PROTPARS:protpars
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arg:PREEDIT
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argtype:chooser
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arglabel:Edit input before running?
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argchoice:No:
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argchoice:Yes:kedit infile;
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in:in1
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informat:genbank
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inmask:
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insave:
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item:Phylip DNA Distance methods
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itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ;$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)&
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arg:EXPLAIN
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argtype:text
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arglabel:To produce a bootstraped tree choose DNADIST+NEIGHOR+CONSENSE
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arg:PROGRAM
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arglabel:Which method?
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argtype:chooser
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argchoice:DNADIST+NEIGHBOR:
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argchoice:DNADIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense;
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arg:PROG
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arglabel:Run ?
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argtype:chooser
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argchoice:Run without Bootstrap:
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argchoice:Run with Bootstrap: /usr/bin/X11/xterm -e seqboot;
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arg:DNA
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argtype:text
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arglabel:Name of DNADIST outfile?
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arg:NEI
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argtype:text
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arglabel:Name of NEIGHBOR outfile?
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arg:TREE
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argtype:text
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arglabel:Name of TREEFILE ?
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arg:PREEDIT
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argtype:chooser
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arglabel:Edit input before running?
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argchoice:No:
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argchoice:Yes:kedit infile;
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in:in1
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informat:genbank
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inmask:
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insave:
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item:Phylip PROTEIN Distance methods
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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)&
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arg:PROGRAM
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|
arglabel:Which method?
|
|
argtype:chooser
|
|
argchoice:PROTDIST+NEIGHBOR:
|
|
argchoice:PROTDIST+NEIGHOR+CONSENSE: /usr/bin/X11/xterm -e consense;
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arg:PROG
|
|
arglabel:Which method?
|
|
argtype:chooser
|
|
argchoice:Bootstrap: /usr/bin/X11/xterm -e seqboot;
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|
argchoice:No Bootstrap:
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arg:PREEDIT
|
|
argtype:chooser
|
|
arglabel:Edit input before running?
|
|
argchoice:No:
|
|
argchoice:Yes:kedit infile;
|
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in:in1
|
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informat:genbank
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inmask:
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insave:
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menu:On-Line Res.
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item:GDE for Linux resources at Bioafrica.net
|
|
itemmethod:netscape http://www.bioafrica.net &
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item:-------------------------
|
|
item:add a new website
|
|
itemmethod:xterm -e /usr/local/biotools/GDE/newURL.pl $name $url
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|
|
arg:name
|
|
argtype:text
|
|
arglabel:Enter the site name
|
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|
|
arg:url
|
|
argtype:text
|
|
arglabel:Enter the URL (including http://)
|