2023-04-16 21:11:03 +08:00
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menu:File
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2022-03-08 04:43:05 +08:00
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item:test cmask output
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2023-04-16 21:11:03 +08:00
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itemmethod: textedit in1
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2022-03-08 04:43:05 +08:00
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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: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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2023-04-16 21:11:03 +08:00
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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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2022-03-08 04:43:05 +08:00
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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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2023-04-16 21:11:03 +08:00
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argchoice:Yes:textedit in1.rpt&
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2022-03-08 04:43:05 +08:00
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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: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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2023-04-16 21:11:03 +08:00
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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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2022-03-08 04:43:05 +08:00
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#Menu for DNA/RNA
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item:blastn
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2023-04-16 21:11:03 +08:00
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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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2022-03-08 04:43:05 +08:00
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in:in1
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informat:flat
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insave:
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2023-04-16 21:11:03 +08:00
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arg:BLASTDB
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2022-03-08 04:43:05 +08:00
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argtype:choice_list
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arglabel:Which Database
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2023-04-16 21:11:03 +08:00
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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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2022-03-08 04:43:05 +08:00
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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
|
2023-04-16 21:11:03 +08:00
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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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2022-03-08 04:43:05 +08:00
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in:in1
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informat:flat
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insave:
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2023-04-16 21:11:03 +08:00
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arg:BLASTDB
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2022-03-08 04:43:05 +08:00
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argtype:choice_list
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arglabel:Which Database
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2023-04-16 21:11:03 +08:00
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argchoice:pir1:$GDE_HELP_DIR/BLAST/pir
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2022-03-08 04:43:05 +08:00
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argchoice:genpept:$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
|
2023-04-16 21:11:03 +08:00
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argchoice:PAM120:PAM120
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argchoice:PAM250:PAM250
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2022-03-08 04:43:05 +08:00
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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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|
2023-04-16 21:11:03 +08:00
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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 $DBASE > in1.out; textedit in1.out;\rm in1*) &
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itemhelp:FASTA.help
|
2022-03-08 04:43:05 +08:00
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2023-04-16 21:11:03 +08:00
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in:in1
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informat:flat
|
2022-03-08 04:43:05 +08:00
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2023-04-16 21:11:03 +08:00
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arg:DBASE
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argtype:choice_list
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arglabel:Database
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argchoice:GenBank Primate:$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
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
|
|
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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 $GDE_HELP_DIR/FASTA/MATRIX/prot.mat
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
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|
menu:Protein
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
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item:Clustal Protein Alignment
|
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|
itemmethod:(tr '%#"' '>' <in1>clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$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
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
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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
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
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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
|
2022-03-08 04:43:05 +08:00
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2023-04-16 21:11:03 +08:00
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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
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
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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:
|
2022-03-08 04:43:05 +08:00
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|
#Menu for Protein
|
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|
2023-04-16 21:11:03 +08:00
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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=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)&
|
2022-03-08 04:43:05 +08:00
|
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in:in1
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informat:flat
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insave:
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|
2023-04-16 21:11:03 +08:00
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arg:BLASTDB
|
2022-03-08 04:43:05 +08:00
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argtype:choice_list
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arglabel:Which Database
|
2023-04-16 21:11:03 +08:00
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argchoice:pir:$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
|
2022-03-08 04:43:05 +08:00
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arg:Matrix
|
2023-04-16 21:11:03 +08:00
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|
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arglabel:Substitution Matrix:
|
2022-03-08 04:43:05 +08:00
|
|
|
argtype:choice_list
|
2023-04-16 21:11:03 +08:00
|
|
|
argchoice:PAM120:PAM120
|
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|
argchoice:PAM250:PAM250
|
2022-03-08 04:43:05 +08:00
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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
|
2023-04-16 21:11:03 +08:00
|
|
|
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???)&
|
2022-03-08 04:43:05 +08:00
|
|
|
|
|
|
|
|
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
|
|
|
|
|
argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank
|
|
|
|
|
argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate
|
|
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|
|
|
|
|
|
|
arg:Matrix
|
|
|
|
|
arglabel:Substitution Matrix:
|
|
|
|
|
argtype:choice_list
|
2023-04-16 21:11:03 +08:00
|
|
|
argchoice:PAM120:PAM120
|
|
|
|
|
argchoice:PAM250:PAM250
|
2022-03-08 04:43:05 +08:00
|
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|
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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
|
|
|
|
|
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
|
|
|
|
|
|
2023-04-16 21:11:03 +08:00
|
|
|
item:blast3
|
|
|
|
|
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)&
|
|
|
|
|
|
|
|
|
|
in:in1
|
|
|
|
|
informat:flat
|
|
|
|
|
insave:
|
|
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|
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|
|
|
|
|
arg:BLASTDB
|
|
|
|
|
argtype:choice_list
|
|
|
|
|
arglabel:Which Database
|
|
|
|
|
argchoice:pir1:$GDE_HELP_DIR/BLAST/pir
|
|
|
|
|
argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
|
|
|
|
|
|
|
|
|
|
arg:Matrix
|
|
|
|
|
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
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informat:flat
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out:out1
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outformat:gde
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outoverwrite:
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2022-03-08 04:43:05 +08:00
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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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|
2023-04-16 21:11:03 +08:00
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item:Restriction sites
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itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp);
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itemhelp:Restriction.help
|
2022-03-08 04:43:05 +08:00
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2023-04-16 21:11:03 +08:00
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arg:ENZ
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2022-03-08 04:43:05 +08:00
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argtype:text
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2023-04-16 21:11:03 +08:00
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arglabel:Enzyme file
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argtext:$GDE_HELP_DIR/DATA_FILES/enzymes
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arg:PRE_EDIT
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argtype:chooser
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arglabel:Edit enzyme file first?
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argchoice:Yes:textedit in1.tmp;
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argchoice:No:
|
2022-03-08 04:43:05 +08:00
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2023-04-16 21:11:03 +08:00
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in:in1
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informat:flat
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out:out1
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outformat:colormask
|
2022-03-08 04:43:05 +08:00
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menu:Phylogeny
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|
2023-04-16 21:11:03 +08:00
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item:DeSoete Tree fit
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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* )&
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itemhelp:lsadt.help
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in:in1
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informat:genbank
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insave:
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inmask:
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arg:CORR
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arglabel:Distance correction?
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argtype:chooser
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argchoice:Olsen:-c=olsen
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argchoice:Jukes/Cantor:-c=jukes
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argchoice:None:-c=none
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arg:INIT
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arglabel:Initial parameter estimate
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argtype:choice_list
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argchoice:uniformly distributed random numbers:1
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argchoice:error-perturbed data:2
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argchoice:original distance data from input matrix:3
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arg:SEED
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argtype:slider
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arglabel:Random number seed
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argmin:0
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argmax:65535
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argvalue:12345
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arg:DISPLAY_FUNC
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argtype:chooser
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arglabel:View tree using
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argchoice:TextEdit:textedit
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argchoice:Treetool:treetool <
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|
2022-03-08 04:43:05 +08:00
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item:Phylip help
|
2023-04-16 21:11:03 +08:00
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itemmethod:(textedit $GDE_HELP_DIR/PHYLIP/$FILE)&
|
2022-03-08 04:43:05 +08:00
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arg:FILE
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argtype:choice_list
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arglabel:Which program?
|
2023-04-16 21:11:03 +08:00
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argchoice:boot:boot.doc
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argchoice:clique:clique.doc
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argchoice:consense:consense.doc
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argchoice:contchar:contchar.doc
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argchoice:contml:contml.doc
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argchoice:contrast:contrast.doc
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argchoice:discrete:discrete.doc
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argchoice:distance:distance.doc
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argchoice:dnaboot:dnaboot.doc
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argchoice:dnacomp:dnacomp.doc
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argchoice:dnadist:dnadist.doc
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argchoice:dnainvar:dnainvar.doc
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argchoice:dnaml:dnaml.doc
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argchoice:dnamlk:dnamlk.doc
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argchoice:dnamove:dnamove.doc
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argchoice:dnapars:dnapars.doc
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argchoice:dnapenny:dnapenny.doc
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argchoice:dolboot:dolboot.doc
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argchoice:dollop:dollop.doc
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argchoice:dolmove:dolmove.doc
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argchoice:dolpenny:dolpenny.doc
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argchoice:draw:draw.doc
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argchoice:drawgram:drawgram.doc
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argchoice:drawtree:drawtree.doc
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argchoice:factor:factor.doc
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argchoice:fitch:fitch.doc
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argchoice:gendist:gendist.doc
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argchoice:kitsch:kitsch.doc
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argchoice:main:main.doc
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argchoice:mix:mix.doc
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argchoice:move:move.doc
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argchoice:neighbor:neighbor.doc
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argchoice:penny:penny.doc
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argchoice:protpars:protpars.doc
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argchoice:read.me.general:read.me.general.doc
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argchoice:restml:restml.doc
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argchoice:seqboot:seqboot.doc
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argchoice:sequence:sequence.doc
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item:Phylip 3.4
|
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itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT shelltool $PROGRAM;textedit outfile;rm in1 )&
|
2022-03-08 04:43:05 +08:00
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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:
|
2023-04-16 21:11:03 +08:00
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argchoice:Yes:textedit infile;
|
2022-03-08 04:43:05 +08:00
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in:in1
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informat:genbank
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inmask:
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insave:
|
2023-04-16 21:11:03 +08:00
|
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item:Phylip Distance methods
|
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|
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)&
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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:mv -f infile outfile;
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argchoice:Fitch:shelltool fitch;
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argchoice:Kitsch:shelltool kitsch;
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argchoice:Neighbor:shelltool neighbor;
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
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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:textedit infile;
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in:in1
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informat:genbank
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inmask:
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insave:
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
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menu:Email
|
2022-03-08 04:43:05 +08:00
|
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|
|
2023-04-16 21:11:03 +08:00
|
|
|
item:BLASTN
|
|
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|
|
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) &
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
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arg:DBASE
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|
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argtype:choice_list
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arglabel:Which Database?
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argchoice:GenBank Qtrly & Updates:GenBank
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argchoice:EMBL:embl
|
2022-03-08 04:43:05 +08:00
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|
2023-04-16 21:11:03 +08:00
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arg:MSCORE
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argtype:slider
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arglabel:Match Score
|
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argmin:3
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argmax:7
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argvalue:5
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in:in1
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informat:flat
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insave:
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item:BLASTP
|
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|
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) &
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arg:DBASE
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|
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argtype:choice_list
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arglabel:Which Database?
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argchoice:Swiss-Prot:swiss-prot
|
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argchoice:PIR:pir
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in:in1
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informat:flat
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insave:
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item:Fasta-(DNA)
|
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|
|
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) &
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arg:DBASE
|
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|
|
argtype:choice_list
|
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|
|
arglabel:Which GenBank Database?
|
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|
|
argchoice:Qrtly & Updates:GenBank/all
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argchoice:Updates:GenBank/new
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argchoice:Primate:GenBank/primate
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argchoice:Rodent:GenBank/rodent
|
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argchoice:Other-Mammalian:GenBank/other_mammalian
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argchoice:Other-Vertebrate:GenBank/other_vertebrate
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argchoice:Invertebrate:GenBank/invertebrate
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argchoice:Plant:GenBank/plant
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argchoice:Organelle:GenBank/organelle
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argchoice:Bacterial:GenBank/bacterial
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argchoice:Structural-RNA:GenBank/structural_rna
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argchoice:Viral:GenBank/viral
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argchoice:Phage:GenBank/phage
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argchoice:Synthetic:GenBank/synthetic
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argchoice:Unannotated:GenBank/unannotated
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arg:KPL
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argtype:slider
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arglabel:K-tuple window
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argmin:3
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argmax:6
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argvalue:4
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arg:TOP
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|
argtype:slider
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|
arglabel:Scores Displayed?
|
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|
argmin:1
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argmax:200
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|
argvalue:100
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|
arg:ALNG
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|
argtype:slider
|
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|
arglabel:# Alignments Displayed?
|
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|
argmin:1
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|
argmax:200
|
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|
argvalue:20
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in:in1
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|
informat:flat
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insave:
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|
item:Fasta-(PROTEIN)
|
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|
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) &
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|
arg:DBASE
|
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|
argtype:choice_list
|
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|
arglabel:Which Protein Database?
|
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|
argchoice:Trans GenBank Qrtly:GenPept/all
|
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|
argchoice:Trans GenBank Daily:GenPept/new
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argchoice:Swiss-Protein:SWISS-PROT/all
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arg:TPL
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|
argtype:slider
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|
arglabel:K-TUP window
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|
argmin:1
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|
argmax:2
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argvalue:1
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|
arg:SCRS
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|
argtype:slider
|
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|
arglabel:# Scores Displayed?
|
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|
argmin:1
|
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|
argmax:200
|
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|
argvalue:100
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|
arg:ALNMNTS
|
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|
argtype:slider
|
|
|
|
|
arglabel:# Alignments Displayed?
|
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|
|
argmin:1
|
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|
|
argmax:200
|
|
|
|
|
argvalue:20
|
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|
in:in1
|
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|
informat:flat
|
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|
insave:
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|
|
item:GeneID
|
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|
|
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) &
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|
|
arg:REPRINT
|
2022-03-08 04:43:05 +08:00
|
|
|
argtype:chooser
|
2023-04-16 21:11:03 +08:00
|
|
|
arglabel:Do you want a GENEID reprint?
|
|
|
|
|
argchoice:YES:echo "Preprint Request" >> in1.tmp
|
|
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|
|
argchoice:NO
|
2022-03-08 04:43:05 +08:00
|
|
|
|
2023-04-16 21:11:03 +08:00
|
|
|
in:in1
|
|
|
|
|
informat:flat
|
|
|
|
|
insave:
|
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|
|
|
|
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|
|
|
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) &
|
|
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|
|
|
|
|
|
|
arg:REGISTER
|
2022-03-08 04:43:05 +08:00
|
|
|
argtype:chooser
|
2023-04-16 21:11:03 +08:00
|
|
|
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:
|
2022-03-08 04:43:05 +08:00
|
|
|
|
2023-04-16 21:11:03 +08:00
|
|
|
item:Grail Registration
|
|
|
|
|
itemmethod:(echo Register > in1.tmp; echo $NAME >> in1.tmp; echo $ADDRESS >> in1.tmp; echo $PHONE >> in1.tmp; echo $EMAIL >> in1.tmp; Mail grail@ornl.gov < in1.tmp; rm in1.tmp)
|
|
|
|
|
|
|
|
|
|
arg:NAME
|
2022-03-08 04:43:05 +08:00
|
|
|
argtype:text
|
2023-04-16 21:11:03 +08:00
|
|
|
arglabel:Your Name
|
2022-03-08 04:43:05 +08:00
|
|
|
|
2023-04-16 21:11:03 +08:00
|
|
|
arg:ADDRESS
|
2022-03-08 04:43:05 +08:00
|
|
|
argtype:text
|
2023-04-16 21:11:03 +08:00
|
|
|
arglabel:Your Address
|
2022-03-08 04:43:05 +08:00
|
|
|
|
2023-04-16 21:11:03 +08:00
|
|
|
arg:PHONE
|
2022-03-08 04:43:05 +08:00
|
|
|
argtype:text
|
2023-04-16 21:11:03 +08:00
|
|
|
arglabel:Your Phone Number
|
|
|
|
|
|
|
|
|
|
arg:EMAIL
|
|
|
|
|
argtype:text
|
|
|
|
|
arglabel:Your E-Mail Address
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
#
|
|
|
|
|
# dgg added new readseq formats, 29 dec 92
|
|
|
|
|
#
|
|
|
|
|
|
|
|
|
|
item:Export Foreign Format
|
|
|
|
|
itemmethod:readseq in1 -pipe -all -form=$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?
|
2022-03-08 04:43:05 +08:00
|
|
|
|
|
|
|
|
in:in1
|
|
|
|
|
informat:genbank
|
|
|
|
|
|
2023-04-16 21:11:03 +08:00
|
|
|
|
|
|
|
|
#
|
|
|
|
|
#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
|
2022-03-08 04:43:05 +08:00
|
|
|
argtype:chooser
|
2023-04-16 21:11:03 +08:00
|
|
|
arglabel:Names at top ?
|
|
|
|
|
argchoice:No:
|
|
|
|
|
argchoice:Yes:-nametop
|
2022-03-08 04:43:05 +08:00
|
|
|
|
2023-04-16 21:11:03 +08:00
|
|
|
arg:NAMELEFT
|
2022-03-08 04:43:05 +08:00
|
|
|
argtype:chooser
|
2023-04-16 21:11:03 +08:00
|
|
|
arglabel:Names at left ?
|
|
|
|
|
argchoice:No:
|
|
|
|
|
argchoice:Yes:-nameleft
|
2022-03-08 04:43:05 +08:00
|
|
|
|
2023-04-16 21:11:03 +08:00
|
|
|
arg:NAMERIGHT
|
2022-03-08 04:43:05 +08:00
|
|
|
argtype:chooser
|
2023-04-16 21:11:03 +08:00
|
|
|
arglabel:Names at right?
|
|
|
|
|
argchoice:Yes:-nameright
|
2022-03-08 04:43:05 +08:00
|
|
|
argchoice:No:
|
2023-04-16 21:11:03 +08:00
|
|
|
|
|
|
|
|
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
|
2022-03-08 04:43:05 +08:00
|
|
|
|
