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Last change
on this file was
5077,
checked in by westram, 16 years ago
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Property svn:eol-style set to
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Property svn:keywords set to
Author Date Id Revision
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File size:
1.3 KB
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| 1 | item:Protein_ML (molphy; max 40 species) |
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| 2 | seqtype: A |
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| 3 | itemmeta: L |
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| 4 | itemmethod:(GEN_INFILE(in1);\ |
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| 5 | cat infile |tr '?' '-' >in1.in;\ |
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| 6 | mv in1.in infile;\ |
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| 7 | RUN_IN_WINDOW((arb_protml $MODEL $SEARCH $REARRANGE $CALCLENGTH infile ;\ |
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| 8 | (test -f treefile && $DISPLAY_FUNC)));\ |
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| 9 | RM_LOCAL_FILES(in1))& |
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| 10 | itemhelp:protml.help |
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| 11 | |
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| 12 | arg:DISPLAY_FUNC |
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| 13 | argtype:choice_menu |
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| 14 | arglabel:What to do with the tree? |
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| 15 | argchoice:ARB ('tree_protml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_protml_$$ treefile "PRG=protml MODEL=$MODEL SEARCH=$SEARCH FILTER=$FILTER REARRANGE=$REARRANGE PKG=molphy" |
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| 16 | argchoice:TextEdit:arb_textedit treefile & |
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| 17 | argchoice:Treetool:treetool treefile |
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| 18 | |
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| 19 | arg:MODEL |
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| 20 | argtype:choice_menu |
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| 21 | arglabel:Which model to use ? |
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| 22 | argchoice:JTT:-j |
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| 23 | argchoice:Dayhoff:-d |
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| 24 | argchoice:mtREV24:-m |
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| 25 | argchoice:Poisson:-p |
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| 26 | argchoice:JTT-F:-jf |
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| 27 | argchoice:Dayhoff-F:-df |
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| 28 | argchoice:mtREV24-F:-mf |
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| 29 | argchoice:Proportional:-pf |
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| 30 | |
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| 31 | arg:SEARCH |
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| 32 | argtype:choice_menu |
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| 33 | arglabel:Search strategy |
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| 34 | argchoice:Star decomposition:-s |
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| 35 | argchoice:Exhaustive:-e |
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| 36 | argchoice:Quick add:-q |
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| 37 | |
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| 38 | arg:CALCLENGTH |
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| 39 | argtype:choice_menu |
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| 40 | arglabel:Calc branchlengths? |
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| 41 | argchoice:Yes:1 |
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| 42 | argchoice:No:0 |
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| 43 | |
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| 44 | arg:REARRANGE |
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| 45 | argtype:choice_menu |
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| 46 | arglabel:Rearrangement |
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| 47 | argchoice:None:0 |
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| 48 | argchoice:local Rearrangement search:-R |
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| 49 | argchoice:LBP only:-RX |
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| 50 | |
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| 51 | in:in1 |
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| 52 | informat:genbank |
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| 53 | inmask: |
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| 54 | insave: |
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