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Last change
on this file was
2,
checked in by oldcode, 24 years ago
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Initial revision
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Property svn:eol-style set to
native
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Property svn:keywords set to
Author Date Id Revision
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File size:
851 bytes
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| 1 | item:Clustal Protein Alignment |
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| 2 | itemmethod:(tr '"%//' '>' <in1 >clus_in;cp in1 test; RUN_IN_WINDOW((clustalv /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Matrx /fixedgap=$FIXED /floatgap=$FLOAT;cat clus_in.pir |sed "s/^>DL;/#/g" |sed "s/^\*$//g" >out1; )); /bin/rm -f clus_in* in1) |
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| 3 | |
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| 4 | |
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| 5 | itemhelp:clustal_help |
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| 6 | |
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| 7 | arg:KTUP |
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| 8 | argtype:slider |
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| 9 | arglabel:K-tuple size for pairwise search |
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| 10 | argmin:1 |
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| 11 | argmax:10 |
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| 12 | argvalue:2 |
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| 13 | |
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| 14 | arg:WIN |
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| 15 | argtype:slider |
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| 16 | arglabel:Window size |
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| 17 | argmin:1 |
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| 18 | argmax:10 |
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| 19 | argvalue:4 |
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| 20 | |
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| 21 | arg:Matrx |
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| 22 | argtype:chooser |
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| 23 | arglabel:Weighting matrix |
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| 24 | argchoice:PAM 250:PAM250 |
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| 25 | argchoice:PAM 100:PAM100 |
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| 26 | argchoice:Identity:ID |
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| 27 | |
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| 28 | arg:FIXED |
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| 29 | argtype:slider |
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| 30 | arglabel:Fixed gap penalty |
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| 31 | argmin:1 |
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| 32 | argmax:100 |
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| 33 | argvalue:10 |
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| 34 | |
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| 35 | arg:FLOAT |
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| 36 | arglabel:Floating gap penalty |
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| 37 | argtype:slider |
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| 38 | argmin:1 |
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| 39 | argmax:100 |
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| 40 | argvalue:10 |
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| 41 | |
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| 42 | |
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| 43 | |
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| 44 | in:in1 |
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| 45 | informat:flat |
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| 46 | insave: |
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| 47 | |
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| 48 | out:out1 |
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| 49 | outformat:flat |
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