| 1 | menu:File |
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| 2 | |
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| 3 | item:New sequence <meta N> |
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| 4 | itemmethod:echo "$Type$Name" > out1 |
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| 5 | itemmeta:n |
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| 6 | itemhelp:new_sequence.help |
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| 7 | |
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| 8 | arg:Name |
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| 9 | argtype:text |
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| 10 | arglabel:New Sequence name? |
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| 11 | argtext:New |
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| 12 | |
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| 13 | arg:Type |
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| 14 | argtype:choice_menu |
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| 15 | arglabel:Type? |
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| 16 | argchoice:DNA/RNA:# |
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| 17 | argchoice:Amino Acid:% |
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| 18 | argchoice:Text:\" |
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| 19 | argchoice:Mask:@ |
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| 20 | |
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| 21 | out:out1 |
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| 22 | outformat:flat |
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| 23 | |
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| 24 | item:Import Foreign Format |
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| 25 | itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp |
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| 26 | itemhelp:readseq.help |
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| 27 | |
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| 28 | arg:INPUTFILE |
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| 29 | argtype:text |
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| 30 | arglabel:Name of foreign file? |
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| 31 | |
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| 32 | out:OUTPUTFILE |
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| 33 | outformat:genbank |
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| 34 | |
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| 35 | item:Export Foreign Format |
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| 36 | itemmethod:readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE |
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| 37 | itemhelp:readseq.help |
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| 38 | |
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| 39 | arg:FORMAT |
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| 40 | argtype:choice_menu |
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| 41 | argchoice:GenBank:genbank |
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| 42 | argchoice:IG/Stanford:ig |
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| 43 | argchoice:NBRF:nbrf |
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| 44 | argchoice:EMBL:embl |
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| 45 | argchoice:GCG:gcg |
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| 46 | argchoice:DNA Strider:strider |
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| 47 | argchoice:Fitch:fitch |
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| 48 | argchoice:Pearson/Fasta:pearson |
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| 49 | argchoice:Zuker:zuker |
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| 50 | argchoice:Olsen:olsen |
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| 51 | argchoice:Phylip:phylip |
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| 52 | argchoice:Plain text:raw |
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| 53 | argchoice:ASN.1:asn |
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| 54 | argchoice:PIR:pir |
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| 55 | argchoice:MSF:msf |
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| 56 | argchoice:PAUP:paup |
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| 57 | argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop |
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| 58 | |
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| 59 | arg:OUTPUTFILE |
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| 60 | argtype:text |
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| 61 | arglabel:Save as? |
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| 62 | |
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| 63 | in:in1 |
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| 64 | informat:genbank |
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| 65 | |
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| 66 | |
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| 67 | item:Save Selection |
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| 68 | itemmethod: cat $SAVE_FUNC > $Name |
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| 69 | itemhelp:save_selection.help |
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| 70 | |
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| 71 | arg:SAVE_FUNC |
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| 72 | argtype:chooser |
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| 73 | arglabel:File format |
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| 74 | argchoice:Flat:in1 |
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| 75 | argchoice:Genbank:in2 |
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| 76 | argchoice:GDE/HGL:in3 |
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| 77 | |
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| 78 | arg:Name |
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| 79 | argtype:text |
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| 80 | arglabel:File name? |
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| 81 | |
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| 82 | in:in1 |
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| 83 | informat:flat |
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| 84 | |
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| 85 | in:in2 |
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| 86 | informat:genbank |
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| 87 | |
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| 88 | in:in3 |
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| 89 | informat:gde |
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| 90 | |
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| 91 | # |
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| 92 | #dgg addition for new readseq, 24 dec 92 |
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| 93 | # |
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| 94 | |
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| 95 | item:Pretty Print |
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| 96 | itemmethod:readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (${ARB_TEXTEDIT:-textedit} in1.pretty; /bin/rm -f in1 in1.pretty)& |
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| 97 | itemhelp:readseq.help |
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| 98 | in:in1 |
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| 99 | informat:genbank |
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| 100 | |
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| 101 | arg:NAMETOP |
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| 102 | argtype:chooser |
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| 103 | arglabel:Names at top ? |
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| 104 | argchoice:No: |
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| 105 | argchoice:Yes:-nametop |
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| 106 | |
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| 107 | arg:NAMELEFT |
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| 108 | argtype:chooser |
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| 109 | arglabel:Names at left ? |
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| 110 | argchoice:No: |
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| 111 | argchoice:Yes:-nameleft |
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| 112 | |
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| 113 | arg:NAMERIGHT |
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| 114 | argtype:chooser |
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| 115 | arglabel:Names at right? |
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| 116 | argchoice:Yes:-nameright |
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| 117 | argchoice:No: |
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| 118 | |
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| 119 | arg:NUMTOP |
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| 120 | argtype:chooser |
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| 121 | arglabel:Numbers at top ? |
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| 122 | argchoice:Yes:-numtop |
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| 123 | argchoice:No: |
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| 124 | |
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| 125 | arg:NUMBOT |
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| 126 | argtype:chooser |
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| 127 | arglabel:Numbers at tail ? |
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| 128 | argchoice:No: |
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| 129 | argchoice:Yes:-numbot |
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| 130 | |
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| 131 | arg:NUMLEFT |
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| 132 | argtype:chooser |
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| 133 | arglabel:Numbers at left ? |
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| 134 | argchoice:Yes:-numleft |
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| 135 | argchoice:No: |
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| 136 | |
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| 137 | arg:NUMRIGHT |
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| 138 | argtype:chooser |
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| 139 | arglabel:Numbers at right? |
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| 140 | argchoice:Yes:-numright |
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| 141 | argchoice:No: |
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| 142 | |
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| 143 | arg:MATCH |
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| 144 | argtype:chooser |
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| 145 | arglabel:Show difference to current species? |
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| 146 | argchoice:No: |
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| 147 | argchoice:Yes:-match |
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| 148 | |
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| 149 | arg:GAPC |
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| 150 | argtype:chooser |
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| 151 | arglabel:Count gap symbols? |
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| 152 | argchoice:No: |
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| 153 | argchoice:Yes:-gap |
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| 154 | |
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| 155 | arg:WIDTH |
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| 156 | argtype:slider |
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| 157 | arglabel:Sequence width? |
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| 158 | argmin:10 |
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| 159 | argmax:200 |
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| 160 | argvalue:50 |
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| 161 | |
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| 162 | arg:COLS |
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| 163 | argtype:slider |
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| 164 | arglabel:Column spacers? |
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| 165 | argmin:0 |
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| 166 | argmax:50 |
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| 167 | argvalue:10 |
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| 168 | |
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| 169 | item:Print Selection |
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| 170 | itemmethod:(PrintStrat -in in1 -width $WIDTH -scale $SCALE -style $STYLE > in1.tmp; $CMD in1.tmp; /bin/rm -f in1 in1.tmp)& |
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| 171 | itemhelp:PrintStrat.help |
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| 172 | |
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| 173 | arg:STYLE |
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| 174 | arglabel:Printing Style |
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| 175 | argtype:chooser |
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| 176 | argchoice:Poster:poster |
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| 177 | argchoice:Compressed:comp |
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| 178 | |
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| 179 | arg:WIDTH |
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| 180 | argtype:slider |
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| 181 | arglabel:Number of Bases Per Line? |
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| 182 | argmin:10 |
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| 183 | argmax:150 |
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| 184 | argvalue:50 |
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| 185 | |
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| 186 | arg:SCALE |
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| 187 | argtype:slider |
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| 188 | arglabel:Reduce printout by? |
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| 189 | argmin:1 |
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| 190 | argmax:20 |
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| 191 | argvalue:1 |
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| 192 | |
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| 193 | arg:CMD |
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| 194 | argtype:chooser |
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| 195 | argchoice:Lpr:lpr |
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| 196 | argchoice:Enscript Gaudy:enscript -G$LAND $FONT -P$PNTER |
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| 197 | argchoice:Enscript Two column:enscript -2rG -P$PNTER |
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| 198 | argchoice:View in a Texteditor:${ARB_TEXTEDIT:-textedit} |
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| 199 | |
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| 200 | arg:LAND |
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| 201 | arglabel:Landscape for Enscript Gaudy? |
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| 202 | argtype:chooser |
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| 203 | argchoice:No: |
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| 204 | argchoice:Yes:r |
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| 205 | |
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| 206 | arg:FONT |
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| 207 | arglabel:Font for Enscript Gaudy? |
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| 208 | argtype:chooser |
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| 209 | argchoice:Medium:-fCourier10 |
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| 210 | argchoice:Small:-fCourier7 |
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| 211 | argchoice:Large:-fCourier-Bold13 |
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| 212 | |
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| 213 | arg:PNTER |
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| 214 | argtype:text |
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| 215 | arglabel:Which printer? |
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| 216 | argtext:pt |
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| 217 | |
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| 218 | in:in1 |
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| 219 | informat:gde |
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| 220 | insave: |
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| 221 | |
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| 222 | |
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| 223 | menu:Edit |
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| 224 | |
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| 225 | item:Sort |
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| 226 | itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;/bin/rm -f in1*)& |
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| 227 | itemhelp:heapsortHGL.help |
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| 228 | |
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| 229 | arg:PRIM_KEY |
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| 230 | argtype:choice_menu |
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| 231 | argchoice:Group:group-ID |
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| 232 | argchoice:type:type |
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| 233 | argchoice:name:name |
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| 234 | argchoice:Sequence ID:sequence-ID |
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| 235 | argchoice:creator:creator |
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| 236 | argchoice:offset:offset |
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| 237 | arglabel:Primary sort field? |
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| 238 | |
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| 239 | arg:SEC_KEY |
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| 240 | argtype:choice_menu |
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| 241 | argchoice:None: |
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| 242 | argchoice:Group:group-ID |
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| 243 | argchoice:type:type |
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| 244 | argchoice:name:name |
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| 245 | argchoice:Sequence ID:sequence-ID |
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| 246 | argchoice:creator:creator |
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| 247 | argchoice:offset:offset |
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| 248 | arglabel:Secondary sort field? |
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| 249 | |
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| 250 | in:in1 |
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| 251 | informat:gde |
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| 252 | insave: |
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| 253 | |
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| 254 | item:extract |
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| 255 | itemmethod:(gde in1;/bin/rm -f in1)& |
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| 256 | |
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| 257 | in:in1 |
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| 258 | informat:gde |
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| 259 | insave: |
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| 260 | |
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| 261 | menu:DNA/RNA |
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| 262 | |
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| 263 | item:Translate... |
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| 264 | itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE $NOSEP in1 > out1 |
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| 265 | |
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| 266 | arg:FRAME |
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| 267 | argtype:chooser |
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| 268 | arglabel:Which reading frame? |
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| 269 | argchoice:First:1 |
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| 270 | argchoice:Second:2 |
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| 271 | argchoice:Third:3 |
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| 272 | argchoice:All six:6 |
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| 273 | |
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| 274 | arg:MNFRM |
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| 275 | arglabel:Minimum length of NT sequence to translate? |
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| 276 | argtype:slider |
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| 277 | argmin:0 |
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| 278 | argmax:500 |
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| 279 | argvalue:20 |
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| 280 | |
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| 281 | arg:LTRCODE |
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| 282 | argtype:chooser |
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| 283 | arglabel:Translate to: |
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| 284 | argchoice:Single letter codes: |
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| 285 | argchoice:Triple letter codes:-3 |
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| 286 | |
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| 287 | arg:NOSEP |
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| 288 | argtype:chooser |
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| 289 | arglabel: Seperate? |
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| 290 | argchoice:No: |
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| 291 | argchoice:Yes:-sep |
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| 292 | |
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| 293 | arg:TBL |
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| 294 | arglabel:Codon table? |
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| 295 | argtype:chooser |
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| 296 | argchoice:mycoplasma:2 |
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| 297 | argchoice:universal:1 |
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| 298 | argchoice:yeast:3 |
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| 299 | argchoice:Vert. mito.:4 |
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| 300 | |
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| 301 | in:in1 |
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| 302 | informat:gde |
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| 303 | |
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| 304 | out:out1 |
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| 305 | outformat:gde |
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| 306 | |
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| 307 | item:Dot plot |
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| 308 | itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)& |
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| 309 | itemhelp:DotPlotTool.help |
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| 310 | |
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| 311 | in:in1 |
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| 312 | informat:gde |
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| 313 | insave: |
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| 314 | |
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| 315 | item:Clustal alignment |
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| 316 | 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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| 317 | |
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| 318 | itemhelp:clustal_help |
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| 319 | |
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| 320 | arg:KTUP |
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| 321 | argtype:slider |
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| 322 | arglabel:K-tuple size for pairwise search |
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| 323 | argmin:1 |
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| 324 | argmax:10 |
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| 325 | argvalue:2 |
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| 326 | |
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| 327 | arg:WIN |
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| 328 | argtype:slider |
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| 329 | arglabel:Window size |
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| 330 | argmin:1 |
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| 331 | argmax:10 |
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| 332 | argvalue:4 |
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| 333 | |
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| 334 | arg:Trans |
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| 335 | argtype:chooser |
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| 336 | arglabel:Transitions weighted? |
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| 337 | argchoice:Yes:/TRANSIT |
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| 338 | argchoice:No: |
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| 339 | |
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| 340 | arg:FIXED |
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| 341 | argtype:slider |
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| 342 | arglabel:Fixed gap penalty |
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| 343 | argmin:1 |
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| 344 | argmax:100 |
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| 345 | argvalue:10 |
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| 346 | |
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| 347 | arg:FLOAT |
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| 348 | arglabel:Floating gap penalty |
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| 349 | argtype:slider |
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| 350 | argmin:1 |
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| 351 | argmax:100 |
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| 352 | argvalue:10 |
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| 353 | |
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| 354 | arg:REPORT |
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| 355 | argtype:chooser |
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| 356 | arglabel:View assembly report? |
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| 357 | argchoice:No: |
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| 358 | argchoice:Yes:${ARB_TEXTEDIT:-textedit} in1.rpt& |
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| 359 | |
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| 360 | |
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| 361 | in:in1 |
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| 362 | informat:flat |
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| 363 | insave: |
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| 364 | |
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| 365 | item:Variable Positions |
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| 366 | itemmethod:varpos $REV < in1 > out1 |
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| 367 | |
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| 368 | arg:REV |
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| 369 | argtype:chooser |
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| 370 | arglabel:Highlight (darken) |
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| 371 | argchoice:Conserved positions: |
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| 372 | argchoice:variable positions:-rev |
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| 373 | |
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| 374 | in:in1 |
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| 375 | informat:flat |
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| 376 | |
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| 377 | out:out1 |
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| 378 | outformat:colormask |
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| 379 | |
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| 380 | |
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| 381 | item:Find all <meta-f> |
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| 382 | itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1; |
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| 383 | itemhelp:findall.help |
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| 384 | itemmeta:f |
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| 385 | |
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| 386 | arg:SEARCH |
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| 387 | argtype:text |
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| 388 | arglabel:Search String |
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| 389 | |
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| 390 | arg:PRCNT |
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| 391 | argtype:slider |
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| 392 | arglabel:Percent mismatch |
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| 393 | argmin:0 |
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| 394 | argmax:75 |
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| 395 | argvalue:10 |
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| 396 | |
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| 397 | arg:CASE |
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| 398 | argtype:chooser |
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| 399 | arglabel:Case |
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| 400 | argchoice:Upper equals lower: |
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| 401 | argchoice:Upper not equal lower:-case |
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| 402 | |
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| 403 | arg:UT |
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| 404 | argtype:chooser |
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| 405 | arglabel:U equal T? |
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| 406 | argchoice:Yes:-u=t |
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| 407 | argchoice:No: |
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| 408 | argvalue:0 |
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| 409 | |
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| 410 | arg:MAT |
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| 411 | arglabel:Match color |
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| 412 | argtype:choice_menu |
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| 413 | argchoice:yellow:1 |
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| 414 | argchoice:violet:2 |
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| 415 | argchoice:red:3 |
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| 416 | argchoice:aqua:4 |
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| 417 | argchoice:green:5 |
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| 418 | argchoice:blue:6 |
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| 419 | argchoice:grey:11 |
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| 420 | argchoice:black:8 |
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| 421 | argvalue:2 |
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| 422 | |
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| 423 | arg:MIS |
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| 424 | argtype:choice_menu |
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| 425 | arglabel:Mismatch color |
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| 426 | argchoice:yellow:1 |
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| 427 | argchoice:violet:2 |
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| 428 | argchoice:red:3 |
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| 429 | argchoice:aqua:4 |
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| 430 | argchoice:green:5 |
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| 431 | argchoice:blue:6 |
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| 432 | argchoice:grey:11 |
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| 433 | argchoice:black:8 |
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| 434 | argvalue:7 |
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| 435 | |
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| 436 | in:in1 |
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| 437 | informat:flat |
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| 438 | |
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| 439 | out:out1 |
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| 440 | outformat:colormask |
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| 441 | |
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| 442 | item:Sequence Consensus |
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| 443 | itemmethod:(MakeCons in1 $METHOD $MASK > out1) |
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| 444 | itemhelp:MakeCons.help |
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| 445 | |
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| 446 | arg:METHOD |
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| 447 | arglabel:Method |
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| 448 | argtype:chooser |
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| 449 | argchoice:IUPAC:-iupac |
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| 450 | argchoice:Majority:-majority $PERCENT |
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| 451 | |
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| 452 | arg:MASK |
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| 453 | argtype:chooser |
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| 454 | arglabel:Create a new: |
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| 455 | argchoice:Sequence: |
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| 456 | argchoice:Selection Mask: | Consto01mask |
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| 457 | |
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| 458 | arg:PERCENT |
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| 459 | arglabel:Minimum Percentage for Majority |
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| 460 | argtype:slider |
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| 461 | argmin:50 |
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| 462 | argmax:100 |
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| 463 | argvalue:75 |
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| 464 | |
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| 465 | in:in1 |
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| 466 | informat:gde |
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| 467 | |
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| 468 | out:out1 |
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| 469 | outformat:gde |
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| 470 | |
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| 471 | |
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| 472 | item:MFOLD |
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| 473 | 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& ${ARB_TEXTEDIT:-textedit} RegionTable; /bin/rm -f RegionTable out1 seqGB* .GDE.tmp.caps)& |
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| 474 | itemhelp:MFOLD.help |
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| 475 | |
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| 476 | in:seqGB |
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| 477 | informat:genbank |
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| 478 | insave: |
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| 479 | |
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| 480 | arg:METHOD |
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| 481 | argtype:chooser |
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| 482 | arglabel:RNA type |
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| 483 | argchoice:Fold Linear RNA:lrna |
|---|
| 484 | argchoice:Fold Circular RNA:crna |
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| 485 | |
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| 486 | arg:CT |
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| 487 | argtype:text |
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| 488 | arglabel:Pairing(ct) File Name |
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| 489 | argtext:mfold_out |
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| 490 | |
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| 491 | |
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| 492 | item:Draw Secondary structure |
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| 493 | itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) & |
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| 494 | itemhelp:LoopTool.help |
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| 495 | |
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| 496 | arg:TEMPLATE |
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| 497 | argtype:chooser |
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| 498 | arglabel:Use template file ./loop.temp? |
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| 499 | argchoice:No: |
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| 500 | argchoice:Yes:-t loop.temp |
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| 501 | |
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| 502 | in:in1 |
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| 503 | informat:genbank |
|---|
| 504 | insave: |
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| 505 | |
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| 506 | item:Highlight helix |
|---|
| 507 | itemmethod:readseq -a -f8 in1 | sed "s/>HELIX/\"HELIX/" > in1.flat; sho_helix < in1.flat > out1;rm in1.flat |
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| 508 | itemhelp:sho_helix.help |
|---|
| 509 | |
|---|
| 510 | in:in1 |
|---|
| 511 | informat:genbank |
|---|
| 512 | |
|---|
| 513 | out:out1 |
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| 514 | outformat:colormask |
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| 515 | |
|---|
| 516 | |
|---|
| 517 | #Menu for DNA/RNA |
|---|
| 518 | |
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| 519 | item:blastn |
|---|
| 520 | itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; blastn $BLASTDB in1.f W=$WORDLEN M=$MATCH N=$MMSCORE > in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1*)& |
|---|
| 521 | itemhelp:blast.help |
|---|
| 522 | |
|---|
| 523 | in:in1 |
|---|
| 524 | informat:flat |
|---|
| 525 | insave: |
|---|
| 526 | |
|---|
| 527 | arg:BLASTDB |
|---|
| 528 | argtype:choice_menu |
|---|
| 529 | arglabel:Which Database |
|---|
| 530 | argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank |
|---|
| 531 | argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate |
|---|
| 532 | |
|---|
| 533 | arg:WORDLEN |
|---|
| 534 | argtype:slider |
|---|
| 535 | arglabel:Word Size |
|---|
| 536 | argmin:4 |
|---|
| 537 | argmax:18 |
|---|
| 538 | argvalue:12 |
|---|
| 539 | |
|---|
| 540 | arg:MATCH |
|---|
| 541 | argtype:slider |
|---|
| 542 | arglabel:Match Score |
|---|
| 543 | argmin:1 |
|---|
| 544 | argmax:10 |
|---|
| 545 | argvalue:5 |
|---|
| 546 | |
|---|
| 547 | arg:MMSCORE |
|---|
| 548 | argtype:slider |
|---|
| 549 | arglabel:Mismatch Score |
|---|
| 550 | argmin:-10 |
|---|
| 551 | argmax:-1 |
|---|
| 552 | argvalue:-5 |
|---|
| 553 | |
|---|
| 554 | item:blastx |
|---|
| 555 | itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)& |
|---|
| 556 | itemhelp:blast.help |
|---|
| 557 | |
|---|
| 558 | in:in1 |
|---|
| 559 | informat:flat |
|---|
| 560 | insave: |
|---|
| 561 | |
|---|
| 562 | arg:BLASTDB |
|---|
| 563 | argtype:choice_menu |
|---|
| 564 | arglabel:Which Database |
|---|
| 565 | argchoice:pir1:$GDE_HELP_DIR/BLAST/pir |
|---|
| 566 | argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept |
|---|
| 567 | |
|---|
| 568 | arg:WORDLEN |
|---|
| 569 | argtype:slider |
|---|
| 570 | arglabel:Word Size |
|---|
| 571 | argmin:1 |
|---|
| 572 | argmax:5 |
|---|
| 573 | argvalue:3 |
|---|
| 574 | |
|---|
| 575 | arg:Matrix |
|---|
| 576 | arglabel:Substitution Matrix: |
|---|
| 577 | argtype:choice_menu |
|---|
| 578 | argchoice:PAM120:PAM120 |
|---|
| 579 | argchoice:PAM250:PAM250 |
|---|
| 580 | |
|---|
| 581 | arg:CODE |
|---|
| 582 | argtype:choice_menu |
|---|
| 583 | arglabel:Genetic Code |
|---|
| 584 | argchoice:Standard or Universal:0 |
|---|
| 585 | argchoice:Vertebrate Mitochondrial:1 |
|---|
| 586 | argchoice:Yeast Mitochondrial:2 |
|---|
| 587 | argchoice:Mold Mitochondrial and Mycoplasma:3 |
|---|
| 588 | argchoice:Invertebrate Mitochondrial:4 |
|---|
| 589 | argchoice:Ciliate Macronuclear:5 |
|---|
| 590 | argchoice:Protozoan Mitochondrial:6 |
|---|
| 591 | argchoice:Plant Mitochondrial:7 |
|---|
| 592 | argchoice:Echinodermate Mitochondrial:8 |
|---|
| 593 | |
|---|
| 594 | |
|---|
| 595 | item:FASTA (DNA/RNA) |
|---|
| 596 | itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; ${ARB_TEXTEDIT:-textedit} in1.out;\rm in1*) & |
|---|
| 597 | itemhelp:FASTA.help |
|---|
| 598 | |
|---|
| 599 | in:in1 |
|---|
| 600 | informat:flat |
|---|
| 601 | |
|---|
| 602 | arg:DBASE |
|---|
| 603 | argtype:choice_menu |
|---|
| 604 | arglabel:Database |
|---|
| 605 | argchoice:GenBank Primate:$GDE_HELP_DIR/FASTA/GENBANK/gbpri.seq\ 1 |
|---|
| 606 | argchoice:GenBank Rodent:$GDE_HELP_DIR/FASTA/GENBANK/gbrod.seq\ 1 |
|---|
| 607 | argchoice:GenBank all Mammal:$GDE_HELP_DIR/FASTA/GENBANK/gbmam.seq\ 1 |
|---|
| 608 | argchoice:GenBank verteBrates:$GDE_HELP_DIR/FASTA/GENBANK/gbvrt.seq\ 1 |
|---|
| 609 | argchoice:GenBank Inverts:$GDE_HELP_DIR/FASTA/GENBANK/gbinv.seq\ 1 |
|---|
| 610 | argchoice:GenBank pLants:$GDE_HELP_DIR/FASTA/GENBANK/gbpln.seq\ 1 |
|---|
| 611 | argchoice:GenBank Struct RNA:$GDE_HELP_DIR/FASTA/GENBANK/gbrna.seq\ 1 |
|---|
| 612 | argchoice:GenBank euk. Organelles:$GDE_HELP_DIR/FASTA/GENBANK/gborg.seq\ 1 |
|---|
| 613 | argchoice:GenBank phaGe:$GDE_HELP_DIR/FASTA/GENBANK/gbphg.seq\ 1 |
|---|
| 614 | argchoice:GenBank bacTeria:$GDE_HELP_DIR/FASTA/GENBANK/gbbct.seq\ 1 |
|---|
| 615 | argchoice:GenBank sYnthetic:$GDE_HELP_DIR/FASTA/GENBANK/gbsyn.seq\ 1 |
|---|
| 616 | argchoice:GenBank Viral:$GDE_HELP_DIR/FASTA/GENBANK/gbvrl.seq\ 1 |
|---|
| 617 | argchoice:GenBank Unannotated:$GDE_HELP_DIR/FASTA/GENBANK/gbuna.seq\ 1 |
|---|
| 618 | |
|---|
| 619 | arg:NUMOFALN |
|---|
| 620 | argtype:slider |
|---|
| 621 | arglabel:Number of Alignment to Report |
|---|
| 622 | argmin:1 |
|---|
| 623 | argmax:100 |
|---|
| 624 | argvalue:20 |
|---|
| 625 | |
|---|
| 626 | arg:MATRIX |
|---|
| 627 | arglabel:Which SMATRIX |
|---|
| 628 | argtype:choice_menu |
|---|
| 629 | argchoice:Default: |
|---|
| 630 | argchoice:altdiag.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altdiag.mat |
|---|
| 631 | argchoice:altprot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altprot.mat |
|---|
| 632 | argchoice:dna.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/dna.mat |
|---|
| 633 | argchoice:prot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/prot.mat |
|---|
| 634 | |
|---|
| 635 | menu:Protein |
|---|
| 636 | |
|---|
| 637 | item:Clustal Protein Alignment |
|---|
| 638 | itemmethod:(tr '%#"' '>' <in1>clus_in;clustalv /output=PIR /infile=clus_in /align /ktup=$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* )& |
|---|
| 639 | itemhelp:clustal_help |
|---|
| 640 | |
|---|
| 641 | arg:KTUP |
|---|
| 642 | argtype:slider |
|---|
| 643 | arglabel:K-tuple size for pairwise search |
|---|
| 644 | argmin:1 |
|---|
| 645 | argmax:10 |
|---|
| 646 | argvalue:2 |
|---|
| 647 | |
|---|
| 648 | arg:WIN |
|---|
| 649 | argtype:slider |
|---|
| 650 | arglabel:Window size |
|---|
| 651 | argmin:1 |
|---|
| 652 | argmax:10 |
|---|
| 653 | argvalue:4 |
|---|
| 654 | |
|---|
| 655 | arg:Matrx |
|---|
| 656 | argtype:chooser |
|---|
| 657 | arglabel:Weighting matrix |
|---|
| 658 | argchoice:PAM 250:PAM250 |
|---|
| 659 | argchoice:PAM 100:PAM100 |
|---|
| 660 | argchoice:Identity:ID |
|---|
| 661 | |
|---|
| 662 | arg:FIXED |
|---|
| 663 | argtype:slider |
|---|
| 664 | arglabel:Fixed gap penalty |
|---|
| 665 | argmin:1 |
|---|
| 666 | argmax:100 |
|---|
| 667 | argvalue:10 |
|---|
| 668 | |
|---|
| 669 | arg:FLOAT |
|---|
| 670 | arglabel:Floating gap penalty |
|---|
| 671 | argtype:slider |
|---|
| 672 | argmin:1 |
|---|
| 673 | argmax:100 |
|---|
| 674 | argvalue:10 |
|---|
| 675 | |
|---|
| 676 | arg:REPORT |
|---|
| 677 | argtype:chooser |
|---|
| 678 | arglabel:View assembly report? |
|---|
| 679 | argchoice:No: |
|---|
| 680 | argchoice:Yes:${ARB_TEXTEDIT:-textedit} in1.rpt& |
|---|
| 681 | |
|---|
| 682 | in:in1 |
|---|
| 683 | informat:flat |
|---|
| 684 | insave: |
|---|
| 685 | |
|---|
| 686 | #Menu for Protein |
|---|
| 687 | |
|---|
| 688 | item:blastp |
|---|
| 689 | itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)& |
|---|
| 690 | itemhelp:blast.help |
|---|
| 691 | |
|---|
| 692 | in:in1 |
|---|
| 693 | informat:flat |
|---|
| 694 | insave: |
|---|
| 695 | |
|---|
| 696 | arg:BLASTDB |
|---|
| 697 | argtype:choice_menu |
|---|
| 698 | arglabel:Which Database |
|---|
| 699 | argchoice:pir:$GDE_HELP_DIR/BLAST/pir |
|---|
| 700 | argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept |
|---|
| 701 | argchoice:local:$GDE_HELP_DIR/BLAST/local_db |
|---|
| 702 | |
|---|
| 703 | arg:Matrix |
|---|
| 704 | arglabel:Substitution Matrix: |
|---|
| 705 | argtype:choice_menu |
|---|
| 706 | argchoice:PAM120:PAM120 |
|---|
| 707 | argchoice:PAM250:PAM250 |
|---|
| 708 | |
|---|
| 709 | arg:WORDLEN |
|---|
| 710 | argtype:slider |
|---|
| 711 | arglabel:Word Size |
|---|
| 712 | argmin:1 |
|---|
| 713 | argmax:5 |
|---|
| 714 | argvalue:3 |
|---|
| 715 | |
|---|
| 716 | item:tblastn |
|---|
| 717 | itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)& |
|---|
| 718 | itemhelp:blast.help |
|---|
| 719 | |
|---|
| 720 | in:in1 |
|---|
| 721 | informat:flat |
|---|
| 722 | insave: |
|---|
| 723 | |
|---|
| 724 | arg:BLASTDB |
|---|
| 725 | argtype:choice_menu |
|---|
| 726 | arglabel:Which Database |
|---|
| 727 | argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank |
|---|
| 728 | argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate |
|---|
| 729 | |
|---|
| 730 | arg:Matrix |
|---|
| 731 | arglabel:Substitution Matrix: |
|---|
| 732 | argtype:choice_menu |
|---|
| 733 | argchoice:PAM120:PAM120 |
|---|
| 734 | argchoice:PAM250:PAM250 |
|---|
| 735 | |
|---|
| 736 | arg:WORDLEN |
|---|
| 737 | argtype:slider |
|---|
| 738 | arglabel:Word Size |
|---|
| 739 | argmin:4 |
|---|
| 740 | argmax:18 |
|---|
| 741 | argvalue:12 |
|---|
| 742 | |
|---|
| 743 | arg:CODE |
|---|
| 744 | argtype:choice_menu |
|---|
| 745 | arglabel:Genetic Code |
|---|
| 746 | argchoice:Standard or Universal:0 |
|---|
| 747 | argchoice:Vertebrate Mitochondrial:1 |
|---|
| 748 | argchoice:Yeast Mitochondrial:2 |
|---|
| 749 | argchoice:Mold Mitochondrial and Mycoplasma:3 |
|---|
| 750 | argchoice:Invertebrate Mitochondrial:4 |
|---|
| 751 | argchoice:Ciliate Macronuclear:5 |
|---|
| 752 | argchoice:Protozoan Mitochondrial:6 |
|---|
| 753 | argchoice:Plant Mitochondrial:7 |
|---|
| 754 | argchoice:Echinodermate Mitochondrial:8 |
|---|
| 755 | |
|---|
| 756 | item:blast3 |
|---|
| 757 | itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)& |
|---|
| 758 | itemhelp:blast3.help |
|---|
| 759 | |
|---|
| 760 | in:in1 |
|---|
| 761 | informat:flat |
|---|
| 762 | insave: |
|---|
| 763 | |
|---|
| 764 | arg:BLASTDB |
|---|
| 765 | argtype:choice_menu |
|---|
| 766 | arglabel:Which Database |
|---|
| 767 | argchoice:pir1:$GDE_HELP_DIR/BLAST/pir |
|---|
| 768 | argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept |
|---|
| 769 | |
|---|
| 770 | arg:Matrix |
|---|
| 771 | arglabel:Substitution Matrix: |
|---|
| 772 | argtype:choice_menu |
|---|
| 773 | argchoice:PAM120:PAM120 |
|---|
| 774 | argchoice:PAM250:PAM250 |
|---|
| 775 | |
|---|
| 776 | arg:WORDLEN |
|---|
| 777 | argtype:slider |
|---|
| 778 | arglabel:Word Size |
|---|
| 779 | argmin:1 |
|---|
| 780 | argmax:5 |
|---|
| 781 | argvalue:3 |
|---|
| 782 | |
|---|
| 783 | item:FASTA (Protein) |
|---|
| 784 | itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; ${ARB_TEXTEDIT:-textedit} in1.out;\rm in1*) & |
|---|
| 785 | itemhelp:FASTA.help |
|---|
| 786 | |
|---|
| 787 | in:in1 |
|---|
| 788 | informat:flat |
|---|
| 789 | |
|---|
| 790 | arg:DBASE |
|---|
| 791 | argtype:choice_menu |
|---|
| 792 | arglabel:Database |
|---|
| 793 | argchoice:NBRF PIR1:$GDE_HELP_DIR/FASTA/PIR/pir1.dat\ 2 |
|---|
| 794 | argchoice:NBRF PIR2:$GDE_HELP_DIR/FASTA/PIR/pir2.dat\ 2 |
|---|
| 795 | argchoice:NBRF PIR3:$GDE_HELP_DIR/FASTA/PIR/pir3.dat\ 2 |
|---|
| 796 | |
|---|
| 797 | |
|---|
| 798 | arg:NUMOFALN |
|---|
| 799 | argtype:slider |
|---|
| 800 | arglabel:Number of Alignment to Report |
|---|
| 801 | argmin:1 |
|---|
| 802 | argmax:100 |
|---|
| 803 | argvalue:20 |
|---|
| 804 | |
|---|
| 805 | arg:MATRIX |
|---|
| 806 | arglabel:Which SMATRIX |
|---|
| 807 | argtype:choice_menu |
|---|
| 808 | argchoice:Default: |
|---|
| 809 | argchoice:Minimum mutation matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/codaa.mat |
|---|
| 810 | argchoice:Identity matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/idnaa.mat |
|---|
| 811 | argchoice:Identity matrix for mismatches:-s $GDE_HELP_DIR/FASTA/MATRIX/idpaa.mat |
|---|
| 812 | argchoice:PAM250:-s $GDE_HELP_DIR/FASTA/MATRIX/pam250.mat |
|---|
| 813 | argchoice:PAM120:-s $GDE_HELP_DIR/FASTA/MATRIX/pam120.mat |
|---|
| 814 | |
|---|
| 815 | menu:Seq management |
|---|
| 816 | |
|---|
| 817 | item:Assemble Contigs |
|---|
| 818 | itemmethod:(sed "s/#/>/"<in1 >in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp) |
|---|
| 819 | itemhelp:CAP2.help |
|---|
| 820 | |
|---|
| 821 | arg:OVERLAP |
|---|
| 822 | argtype:slider |
|---|
| 823 | arglabel:Minimum overlap? |
|---|
| 824 | argmin:5 |
|---|
| 825 | argmax:100 |
|---|
| 826 | argvalue:20 |
|---|
| 827 | |
|---|
| 828 | arg:PMATCH |
|---|
| 829 | argtype:slider |
|---|
| 830 | arglabel:Percent match required within overlap |
|---|
| 831 | argmin:25 |
|---|
| 832 | argmax:100 |
|---|
| 833 | argvalue:90 |
|---|
| 834 | |
|---|
| 835 | in:in1 |
|---|
| 836 | informat:flat |
|---|
| 837 | |
|---|
| 838 | out:out1 |
|---|
| 839 | outformat:gde |
|---|
| 840 | outoverwrite: |
|---|
| 841 | |
|---|
| 842 | item:Map View |
|---|
| 843 | itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)& |
|---|
| 844 | itemhelp:mapview.help |
|---|
| 845 | |
|---|
| 846 | in:in1 |
|---|
| 847 | informat:gde |
|---|
| 848 | insave: |
|---|
| 849 | |
|---|
| 850 | arg:PBL |
|---|
| 851 | arglabel:Pixel Between Lines |
|---|
| 852 | argtype:slider |
|---|
| 853 | argvalue:10 |
|---|
| 854 | argmin:1 |
|---|
| 855 | argmax:15 |
|---|
| 856 | |
|---|
| 857 | arg:NPP |
|---|
| 858 | arglabel:Nucleotides Per Pixel |
|---|
| 859 | argtype:slider |
|---|
| 860 | argvalue:1 |
|---|
| 861 | argmin:1 |
|---|
| 862 | argmax:20 |
|---|
| 863 | |
|---|
| 864 | arg:LWIDTH |
|---|
| 865 | arglabel:Line Thickness |
|---|
| 866 | argtype:slider |
|---|
| 867 | argvalue:2 |
|---|
| 868 | argmin:1 |
|---|
| 869 | argmax:5 |
|---|
| 870 | |
|---|
| 871 | |
|---|
| 872 | item:Restriction sites |
|---|
| 873 | itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp); |
|---|
| 874 | itemhelp:Restriction.help |
|---|
| 875 | |
|---|
| 876 | arg:ENZ |
|---|
| 877 | argtype:text |
|---|
| 878 | arglabel:Enzyme file |
|---|
| 879 | argtext:$GDE_HELP_DIR/DATA_FILES/enzymes |
|---|
| 880 | |
|---|
| 881 | arg:PRE_EDIT |
|---|
| 882 | argtype:chooser |
|---|
| 883 | arglabel:Edit enzyme file first? |
|---|
| 884 | argchoice:Yes:${ARB_TEXTEDIT:-textedit} in1.tmp; |
|---|
| 885 | argchoice:No: |
|---|
| 886 | |
|---|
| 887 | in:in1 |
|---|
| 888 | informat:flat |
|---|
| 889 | |
|---|
| 890 | out:out1 |
|---|
| 891 | outformat:colormask |
|---|
| 892 | |
|---|
| 893 | menu:Phylogeny |
|---|
| 894 | |
|---|
| 895 | item:DeSoete Tree fit |
|---|
| 896 | 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 ; $DISPLAY_FUNC in1.out;/bin/rm -f in1* )& |
|---|
| 897 | itemhelp:lsadt.help |
|---|
| 898 | |
|---|
| 899 | in:in1 |
|---|
| 900 | informat:genbank |
|---|
| 901 | insave: |
|---|
| 902 | inmask: |
|---|
| 903 | |
|---|
| 904 | arg:CORR |
|---|
| 905 | arglabel:Distance correction? |
|---|
| 906 | argtype:chooser |
|---|
| 907 | argchoice:Olsen:-c=olsen |
|---|
| 908 | argchoice:Jukes/Cantor:-c=jukes |
|---|
| 909 | argchoice:None:-c=none |
|---|
| 910 | |
|---|
| 911 | arg:INIT |
|---|
| 912 | arglabel:Initial parameter estimate |
|---|
| 913 | argtype:choice_menu |
|---|
| 914 | argchoice:uniformly distributed random numbers:1 |
|---|
| 915 | argchoice:error-perturbed data:2 |
|---|
| 916 | argchoice:original distance data from input matrix:3 |
|---|
| 917 | |
|---|
| 918 | arg:SEED |
|---|
| 919 | argtype:slider |
|---|
| 920 | arglabel:Random number seed |
|---|
| 921 | argmin:0 |
|---|
| 922 | argmax:65535 |
|---|
| 923 | argvalue:12345 |
|---|
| 924 | |
|---|
| 925 | arg:DISPLAY_FUNC |
|---|
| 926 | argtype:chooser |
|---|
| 927 | arglabel:View tree using |
|---|
| 928 | argchoice:TextEdit:${ARB_TEXTEDIT:-textedit} |
|---|
| 929 | argchoice:Treetool:treetool |
|---|
| 930 | |
|---|
| 931 | item:Phylip help |
|---|
| 932 | itemmethod:(${ARB_TEXTEDIT:-textedit} $GDE_HELP_DIR/PHYLIP/$FILE)& |
|---|
| 933 | |
|---|
| 934 | arg:FILE |
|---|
| 935 | argtype:choice_menu |
|---|
| 936 | arglabel:Which program? |
|---|
| 937 | argchoice:clique:clique.doc |
|---|
| 938 | argchoice:coallike:coallike.doc |
|---|
| 939 | argchoice:consense:consense.doc |
|---|
| 940 | argchoice:contchar:contchar.doc |
|---|
| 941 | argchoice:contml:contml.doc |
|---|
| 942 | argchoice:contrast:contrast.doc |
|---|
| 943 | argchoice:discrete:discrete.doc |
|---|
| 944 | argchoice:distance:distance.doc |
|---|
| 945 | argchoice:dnacomp:dnacomp.doc |
|---|
| 946 | argchoice:dnadist:dnadist.doc |
|---|
| 947 | argchoice:dnainvar:dnainvar.doc |
|---|
| 948 | argchoice:dnaml:dnaml.doc |
|---|
| 949 | argchoice:dnamlk:dnamlk.doc |
|---|
| 950 | argchoice:dnamove:dnamove.doc |
|---|
| 951 | argchoice:dnapars:dnapars.doc |
|---|
| 952 | argchoice:dnapenny:dnapenny.doc |
|---|
| 953 | argchoice:dollop:dollop.doc |
|---|
| 954 | argchoice:dolmove:dolmove.doc |
|---|
| 955 | argchoice:dolpenny:dolpenny.doc |
|---|
| 956 | argchoice:draw:draw.doc |
|---|
| 957 | argchoice:drawgram:drawgram.doc |
|---|
| 958 | argchoice:drawtree:drawtree.doc |
|---|
| 959 | argchoice:factor:factor.doc |
|---|
| 960 | argchoice:fitch:fitch.doc |
|---|
| 961 | argchoice:gendist:gendist.doc |
|---|
| 962 | argchoice:kitsch:kitsch.doc |
|---|
| 963 | argchoice:main:main.doc |
|---|
| 964 | argchoice:makeinf:makeinf.doc |
|---|
| 965 | argchoice:mix:mix.doc |
|---|
| 966 | argchoice:move:move.doc |
|---|
| 967 | argchoice:neighbor:neighbor.doc |
|---|
| 968 | argchoice:penny:penny.doc |
|---|
| 969 | argchoice:protdist:protdist.doc |
|---|
| 970 | argchoice:protml:protml.doc |
|---|
| 971 | argchoice:protpars:protpars.doc |
|---|
| 972 | argchoice:restml:restml.doc |
|---|
| 973 | argchoice:retree:retree.doc |
|---|
| 974 | argchoice:seqboot:seqboot.doc |
|---|
| 975 | argchoice:sequence:sequence.doc |
|---|
| 976 | |
|---|
| 977 | |
|---|
| 978 | |
|---|
| 979 | item:Phylip 3.5 |
|---|
| 980 | |
|---|
| 981 | itemmethod:(/bin/rm -f outfile infile treefile ; readseq -a -f12 in1 > infile;$PREEDIT $BOOTSTRP ${ARB_XCMD:-cmdtool} $PROGRAM; $CONS ${ARB_TEXTEDIT:-textedit} outfile $DISPLAY_FUNC; rm in1 )& |
|---|
| 982 | |
|---|
| 983 | arg:PROGRAM |
|---|
| 984 | argtype:choice_menu |
|---|
| 985 | arglabel:Which program to run? |
|---|
| 986 | argchoice:DNAPARS:dnapars |
|---|
| 987 | argchoice:DNAML:dnaml |
|---|
| 988 | argchoice:DNAMLK:dnamlk |
|---|
| 989 | argchoice:DNACOMP:dnacomp |
|---|
| 990 | argchoice:DNAMOVE:dnamove |
|---|
| 991 | argchoice:DNAINVAR:dnainvar |
|---|
| 992 | argchoice:PROTPARS:protpars |
|---|
| 993 | #argchoice:PROTML:protml |
|---|
| 994 | |
|---|
| 995 | arg:BOOTSTRP |
|---|
| 996 | arglabel:Bootstrap data? |
|---|
| 997 | argtype:chooser |
|---|
| 998 | argchoice:No: |
|---|
| 999 | argchoice:Yes: ${ARB_XCMD:-cmdtool} seqboot ; /bin/mv -f outfile infile; |
|---|
| 1000 | |
|---|
| 1001 | arg:CONS |
|---|
| 1002 | arglabel:Consensus tree? |
|---|
| 1003 | argtype:chooser |
|---|
| 1004 | argchoice:No: |
|---|
| 1005 | argchoice:Yes: /bin/mv -f treefile infile; ${ARB_XCMD:-cmdtool} consense ; |
|---|
| 1006 | |
|---|
| 1007 | arg:DISPLAY_FUNC |
|---|
| 1008 | argtype:chooser |
|---|
| 1009 | arglabel:View tree using treetool? |
|---|
| 1010 | argchoice:Yes:& treetool treefile |
|---|
| 1011 | argchoice:No: |
|---|
| 1012 | |
|---|
| 1013 | |
|---|
| 1014 | arg:PREEDIT |
|---|
| 1015 | argtype:chooser |
|---|
| 1016 | arglabel:Edit input before running? |
|---|
| 1017 | argchoice:No: |
|---|
| 1018 | argchoice:Yes:${ARB_TEXTEDIT:-textedit} infile; |
|---|
| 1019 | |
|---|
| 1020 | |
|---|
| 1021 | |
|---|
| 1022 | in:in1 |
|---|
| 1023 | informat:genbank |
|---|
| 1024 | inmask: |
|---|
| 1025 | insave: |
|---|
| 1026 | |
|---|
| 1027 | item:Phylip Distance methods |
|---|
| 1028 | itemmethod:(/bin/rm -f treefile infile outfile; readseq -a -f12 in1 > infile ; $PREEDIT ${ARB_XCMD:-cmdtool} $DPGM;mv -f outfile infile;$PROGRAM ${ARB_TEXTEDIT:-textedit} outfile & treetool treefile;/bin/rm -f in1 infile outfile)& |
|---|
| 1029 | |
|---|
| 1030 | arg:PROGRAM |
|---|
| 1031 | arglabel:Which method? |
|---|
| 1032 | argtype:chooser |
|---|
| 1033 | argchoice:DNADIST:mv -f infile outfile; |
|---|
| 1034 | argchoice:Fitch:${ARB_XCMD:-cmdtool} fitch; |
|---|
| 1035 | argchoice:Kitsch:${ARB_XCMD:-cmdtool} kitsch; |
|---|
| 1036 | argchoice:Neighbor:${ARB_XCMD:-cmdtool} neighbor; |
|---|
| 1037 | |
|---|
| 1038 | arg:DPGM |
|---|
| 1039 | arglabel:Treat data as.. |
|---|
| 1040 | argtype:chooser |
|---|
| 1041 | argchoice:DNA:dnadist |
|---|
| 1042 | argchoice:RNA:dnadist |
|---|
| 1043 | argchoice:AA:protdist |
|---|
| 1044 | |
|---|
| 1045 | arg:PREEDIT |
|---|
| 1046 | argtype:chooser |
|---|
| 1047 | arglabel:Edit input before running? |
|---|
| 1048 | argchoice:No: |
|---|
| 1049 | argchoice:Yes:${ARB_TEXTEDIT:-textedit} infile; |
|---|
| 1050 | |
|---|
| 1051 | in:in1 |
|---|
| 1052 | informat:genbank |
|---|
| 1053 | inmask: |
|---|
| 1054 | insave: |
|---|
| 1055 | |
|---|
| 1056 | menu:Email |
|---|
| 1057 | |
|---|
| 1058 | item:Blastn (Nucleic Acid) |
|---|
| 1059 | itemmethod:(echo PROGRAM blastn > in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo HISTOGRAM $PLOT >> in1.tmp; echo ALIGNMENTS $SCORE >> in1.tmp; echo SPLIT 100000 >> in1.tmp; echo BEGIN >> in1.tmp; readseq -i1 -p -f8 in1 >> in1.tmp; cat in1.tmp | /bin/mail blast@ncbi.nlm.nih.gov; rm in1 in1.tmp) & |
|---|
| 1060 | |
|---|
| 1061 | arg:DBASE |
|---|
| 1062 | argtype:choice_menu |
|---|
| 1063 | arglabel:Which Database? |
|---|
| 1064 | argchoice:Non-redundant database:nr |
|---|
| 1065 | argchoice:GenBank DNA sequence database:genbank |
|---|
| 1066 | argchoice:GenBank update (cumulative daily updates):gbupdate |
|---|
| 1067 | argchoice:EMBL DNA sequence database:embl |
|---|
| 1068 | argchoice:EMBL update (cumulative weekly updates):emblu |
|---|
| 1069 | argchoice:Vector subset of GenBank:vector |
|---|
| 1070 | argchoice:Database of Expressed Sequence Tags (ESTs):dbest |
|---|
| 1071 | argchoice:Eukaryotic promoterdatabase:epd |
|---|
| 1072 | argchoice:Kabat's database of immunological interest:kabatnuc |
|---|
| 1073 | |
|---|
| 1074 | arg:PLOT |
|---|
| 1075 | argtype:chooser |
|---|
| 1076 | arglabel:Display Histogram? |
|---|
| 1077 | argvalue:1 |
|---|
| 1078 | argchoice:Yes:yes |
|---|
| 1079 | argchoice:No:no |
|---|
| 1080 | |
|---|
| 1081 | arg:SCORE |
|---|
| 1082 | argtype:slider |
|---|
| 1083 | arglabel:Number of High Scoring Pairs Displayed? |
|---|
| 1084 | argmin:1 |
|---|
| 1085 | argmax:250 |
|---|
| 1086 | argvalue:5 |
|---|
| 1087 | |
|---|
| 1088 | in:in1 |
|---|
| 1089 | informat:genbank |
|---|
| 1090 | insave: |
|---|
| 1091 | |
|---|
| 1092 | item:Blastp (Protein) |
|---|
| 1093 | itemmethod:(echo PROGRAM blastp >in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo HISTOGRAM $PLOT >> in1.tmp; echo ALIGNMENTS $SCORE >> in1.tmp; echo MATRIX $MATRX >> in1.tmp; echo SPLIT 100000 >> in1.tmp; echo BEGIN >> in1.tmp; readseq -i1 -p -f8 in1 >> in1.tmp; cat in1.tmp | /bin/mail blast@ncbi.nlm.nih.gov; rm in1 in1.tmp) & |
|---|
| 1094 | |
|---|
| 1095 | arg:DBASE |
|---|
| 1096 | argtype:choice_menu |
|---|
| 1097 | arglabel:Which Database? |
|---|
| 1098 | argchoice:Non-redundant protein database:nr |
|---|
| 1099 | argchoice:Swiss-Prot protein database:swissprot |
|---|
| 1100 | argchoice:PIR protein database:pir |
|---|
| 1101 | argchoice:Cumulative update to Swiss-Prot major release:spupdate |
|---|
| 1102 | argchoice:GenPept (translated GenBank):genpept |
|---|
| 1103 | argchoice:GenPept update (cumulative daily updates):gpupdate |
|---|
| 1104 | argchoice:Brookhaven PDB:pdb |
|---|
| 1105 | argchoice:Kabat's database of immunological interest:kabatnuc |
|---|
| 1106 | argchoice:Transcription Factors Database:tfd |
|---|
| 1107 | argchoice:6-frame translations of human Alu repeats:palu |
|---|
| 1108 | |
|---|
| 1109 | arg:PLOT |
|---|
| 1110 | argtype:chooser |
|---|
| 1111 | arglabel:Display Histogram? |
|---|
| 1112 | argvalue:1 |
|---|
| 1113 | argchoice:Yes:yes |
|---|
| 1114 | argchoice:No:no |
|---|
| 1115 | |
|---|
| 1116 | arg:SCORE |
|---|
| 1117 | argtype:slider |
|---|
| 1118 | arglabel:Number of High Scoring Pairs Displayed |
|---|
| 1119 | argmin:1 |
|---|
| 1120 | argmax:250 |
|---|
| 1121 | argvalue:5 |
|---|
| 1122 | |
|---|
| 1123 | arg:Matrx |
|---|
| 1124 | argtype:chooser |
|---|
| 1125 | arglabel:Weighting matrix |
|---|
| 1126 | argchoice:PAM 250:PAM250 |
|---|
| 1127 | argchoice:PAM 120:PAM10 |
|---|
| 1128 | argchoice:PAM 40:PAM40 |
|---|
| 1129 | argchoice:BLOSUM62:BLOSUM62 |
|---|
| 1130 | |
|---|
| 1131 | |
|---|
| 1132 | in:in1 |
|---|
| 1133 | informat:genbank |
|---|
| 1134 | insave: |
|---|
| 1135 | |
|---|
| 1136 | item:Fasta (Nucleic Acid) |
|---|
| 1137 | itemmethod:(echo LIB $DBASE > in1.tmp; echo WORD $KPL >> in1.tmp; echo LIST $TOP >> in1.tmp; echo ALIGN $ALNG >> in1.tmp; echo ONE >> in1.tmp; echo SEQ >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp;Mail FASTA@EMBL-Heidelberg.de < in1.tmp; rm in1 in1.tmp) & |
|---|
| 1138 | |
|---|
| 1139 | arg:DBASE |
|---|
| 1140 | argtype:choice_menu |
|---|
| 1141 | arglabel:Which Database? |
|---|
| 1142 | argchoice:GenBank Qrtly & Updates:GBALL |
|---|
| 1143 | argchoice:GenBank Updates:GBNEW |
|---|
| 1144 | argchoice:Entries only in GenBank, not in EMBL:GBONLY |
|---|
| 1145 | argchoice:GenBank and EMBL entries (latest releases):GENEMBL |
|---|
| 1146 | argchoice:New EMBL entries (Since latest release):EMNEW |
|---|
| 1147 | argchoice:All EMBL entries (latest release + new ones):EMALL |
|---|
| 1148 | argchoice:EMBL fungi division only:EFUN |
|---|
| 1149 | argchoice:EMBL invertebrates division only:EINV |
|---|
| 1150 | argchoice:EMBL mammals division only:EMAM |
|---|
| 1151 | argchoice:EMBL organelles division only:EORG |
|---|
| 1152 | argchoice:EMBL phages division only:EPHG |
|---|
| 1153 | argchoice:EMBL plants division only:EPLN |
|---|
| 1154 | argchoice:EMBL primates division only:EPRI |
|---|
| 1155 | argchoice:EMBL prokaryotes division only:EPRO |
|---|
| 1156 | argchoice:EMBL rodents division only:EROD |
|---|
| 1157 | argchoice:EMBL synthetic sequences division only:ESYN |
|---|
| 1158 | argchoice:EMBL unannotated division only:EUNA |
|---|
| 1159 | argchoice:EMBL viruses division only:EVRL |
|---|
| 1160 | argchoice:EMBL vertebrates division only:EVRT |
|---|
| 1161 | |
|---|
| 1162 | |
|---|
| 1163 | |
|---|
| 1164 | arg:KPL |
|---|
| 1165 | argtype:slider |
|---|
| 1166 | arglabel:K-tuple window |
|---|
| 1167 | argmin:3 |
|---|
| 1168 | argmax:6 |
|---|
| 1169 | argvalue:4 |
|---|
| 1170 | |
|---|
| 1171 | arg:TOP |
|---|
| 1172 | argtype:slider |
|---|
| 1173 | arglabel:Scores Displayed? |
|---|
| 1174 | argmin:1 |
|---|
| 1175 | argmax:200 |
|---|
| 1176 | argvalue:100 |
|---|
| 1177 | |
|---|
| 1178 | arg:ALNG |
|---|
| 1179 | argtype:slider |
|---|
| 1180 | arglabel:# Alignments Displayed? |
|---|
| 1181 | argmin:1 |
|---|
| 1182 | argmax:200 |
|---|
| 1183 | argvalue:20 |
|---|
| 1184 | |
|---|
| 1185 | in:in1 |
|---|
| 1186 | informat:flat |
|---|
| 1187 | insave: |
|---|
| 1188 | |
|---|
| 1189 | item:Fasta (Protein) |
|---|
| 1190 | itemmethod:(echo LIB $DBASE > in1.tmp; echo WORD $TPL >> in1.tmp; echo LIST $SCRS >> in1.tmp; echo ALIGN $ALNMNTS >> in1.tmp; echo PROT >> in1.tmp; echo SEQ >> in1.tmp; sed "s/-//g" < in1 | tr '@%#$' '>' >> in1.tmp; Mail FASTA@EMBL-Heidelberg.de < in1.tmp; rm in1 in1.tmp) & |
|---|
| 1191 | |
|---|
| 1192 | arg:DBASE |
|---|
| 1193 | argtype:choice_menu |
|---|
| 1194 | arglabel:Which Protein Database? |
|---|
| 1195 | argchoice:Swiss-Protein (latest release + new ones):SWALL |
|---|
| 1196 | argchoice:Swiss-Protein (since latest release):SWNEW |
|---|
| 1197 | argchoice:Swiss-Protein (latest release):SW |
|---|
| 1198 | argchoice:NBRF/PIR (latest release):NBRF |
|---|
| 1199 | argchoice:NBRF/PIR (not Swiss-Prot):PIRONLY |
|---|
| 1200 | argchoice:All Swiss-Prot and NBRF/PIR entries:SWISSPIRALL |
|---|
| 1201 | argchoice:PDB structure entries:BROOKHAVEN |
|---|
| 1202 | argchoice:PDB structure entries (NBRF version):NRL |
|---|
| 1203 | |
|---|
| 1204 | arg:TPL |
|---|
| 1205 | argtype:slider |
|---|
| 1206 | arglabel:K-TUP window |
|---|
| 1207 | argmin:1 |
|---|
| 1208 | argmax:2 |
|---|
| 1209 | argvalue:1 |
|---|
| 1210 | |
|---|
| 1211 | arg:SCRS |
|---|
| 1212 | argtype:slider |
|---|
| 1213 | arglabel:# Scores Displayed? |
|---|
| 1214 | argmin:1 |
|---|
| 1215 | argmax:200 |
|---|
| 1216 | argvalue:100 |
|---|
| 1217 | |
|---|
| 1218 | arg:ALNMNTS |
|---|
| 1219 | argtype:slider |
|---|
| 1220 | arglabel:# Alignments Displayed? |
|---|
| 1221 | argmin:1 |
|---|
| 1222 | argmax:200 |
|---|
| 1223 | argvalue:20 |
|---|
| 1224 | |
|---|
| 1225 | in:in1 |
|---|
| 1226 | informat:flat |
|---|
| 1227 | insave: |
|---|
| 1228 | |
|---|
| 1229 | item:GeneID |
|---|
| 1230 | 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) & |
|---|
| 1231 | |
|---|
| 1232 | arg:REPRINT |
|---|
| 1233 | argtype:chooser |
|---|
| 1234 | arglabel:Do you want a GENEID reprint? |
|---|
| 1235 | argchoice:YES:echo "Preprint Request" >> in1.tmp |
|---|
| 1236 | argchoice:NO |
|---|
| 1237 | |
|---|
| 1238 | in:in1 |
|---|
| 1239 | informat:flat |
|---|
| 1240 | insave: |
|---|
| 1241 | |
|---|
| 1242 | |
|---|
| 1243 | |
|---|
| 1244 | |
|---|
| 1245 | |
|---|
| 1246 | item:Sequence Retrieval |
|---|
| 1247 | itemmethod:(echo DATALIB $DBASE>> in1.tmp; echo MAXDOCS $NDOC >> in1.tmp;echo MAXLINES 100000 >> in1.tmp; echo BEGIN >> in1.tmp; echo $REGEXP >> in1.tmp; Mail retrieve@ncbi.nlm.nih.gov < in1.tmp; rm in1.tmp) & |
|---|
| 1248 | |
|---|
| 1249 | arg:DBASE |
|---|
| 1250 | argtype:choice_menu |
|---|
| 1251 | arglabel:Which Database? |
|---|
| 1252 | argchoice:GenBank DNA sequence database:genbank |
|---|
| 1253 | argchoice:GenBank update (cumulative daily updates):gbupdate |
|---|
| 1254 | argchoice:EMBL DNA sequence database:embl |
|---|
| 1255 | argchoice:EMBL update (cumulative weekly updates):emblu |
|---|
| 1256 | argchoice:Vector subset of GenBank:vector |
|---|
| 1257 | argchoice:Database of Expressed Sequence Tags (ESTs):dbest |
|---|
| 1258 | argchoice:Swiss-Prot protein database:swissprot |
|---|
| 1259 | argchoice:PIR protein database:pir |
|---|
| 1260 | argchoice:GenPept (translated GenBank):genpept |
|---|
| 1261 | argchoice:GenPept update (cumulative daily updates):gpupdate |
|---|
| 1262 | argchoice:Transcription Factors Database:tfd |
|---|
| 1263 | |
|---|
| 1264 | arg:NDOC |
|---|
| 1265 | argtype:slider |
|---|
| 1266 | arglabel:Number of Sequences Retrieved? |
|---|
| 1267 | argmin:1 |
|---|
| 1268 | argmax:100 |
|---|
| 1269 | argvalue:20 |
|---|
| 1270 | |
|---|
| 1271 | |
|---|
| 1272 | arg:REGEXP |
|---|
| 1273 | argtype:text |
|---|
| 1274 | arglabel:key words, sequence IDs, boolean connectors |
|---|
| 1275 | |
|---|
| 1276 | item:Grail |
|---|
| 1277 | itemmethod:(echo Sequences $TOTALSEQS $ID > in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail grail@ornl.gov <in1.tmp; rm in1 in1.tmp) & |
|---|
| 1278 | |
|---|
| 1279 | arg:REGISTER |
|---|
| 1280 | argtype:chooser |
|---|
| 1281 | arglabel:Have you previously registered for Grail services? |
|---|
| 1282 | argchoice:YES |
|---|
| 1283 | argchoice:NO:echo "YOU MUST REGISTER" |
|---|
| 1284 | |
|---|
| 1285 | arg:TOTALSEQS |
|---|
| 1286 | argtype:text |
|---|
| 1287 | arglabel:Number of Sequences Being Sent to Grail? |
|---|
| 1288 | |
|---|
| 1289 | arg:ID |
|---|
| 1290 | argtype:text |
|---|
| 1291 | arglabel:User ID (MUST HAVE PREVIOUSLY REGISTERED) |
|---|
| 1292 | |
|---|
| 1293 | in:in1 |
|---|
| 1294 | informat:flat |
|---|
| 1295 | insave: |
|---|
| 1296 | |
|---|
| 1297 | item:Grail Registration |
|---|
| 1298 | 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) |
|---|
| 1299 | |
|---|
| 1300 | arg:NAME |
|---|
| 1301 | argtype:text |
|---|
| 1302 | arglabel:Your Name |
|---|
| 1303 | |
|---|
| 1304 | arg:ADDRESS |
|---|
| 1305 | argtype:text |
|---|
| 1306 | arglabel:Your Address |
|---|
| 1307 | |
|---|
| 1308 | arg:PHONE |
|---|
| 1309 | argtype:text |
|---|
| 1310 | arglabel:Your Phone Number |
|---|
| 1311 | |
|---|
| 1312 | arg:EMAIL |
|---|
| 1313 | argtype:text |
|---|
| 1314 | arglabel:Your E-Mail Address |
|---|
| 1315 | |
|---|
| 1316 | |
|---|
