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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
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Property svn:keywords set to
Author Date Id Revision
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File size:
1.5 KB
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| 1 | item:Protein_ML (molphy max 40 species) |
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| 2 | |
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| 3 | itemmethod:(GEN_INFILE(in1);cat infile |tr '?' '-' >in1.in;RUN_IN_WINDOW((CONSFLAG=-consense;$BOOTSTRP;$DISPLAY_FUNC));RM_LOCAL_FILES(in1) )& |
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| 4 | itemhelp:phylip.help |
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| 5 | |
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| 6 | arg:DISPLAY_FUNC |
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| 7 | argtype:chooser |
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| 8 | arglabel:What to do with the tree:? |
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| 9 | argchoice:ARB ('tree_phylip'):arb_read_tree $CONSFLAG tree_ph_$$ protml.tre "PRG=protml PARMETERS=$MODEL$SEARCH FILTER=$FILTER PKG=molphy" |
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| 10 | argchoice:TextEdit:arb_textedit outfile |
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| 11 | argchoice:Treetool:treetool treefile |
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| 12 | |
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| 13 | arg:BOOTSTRP |
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| 14 | arglabel:How many bootstraps ? |
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| 15 | argtype:chooser |
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| 16 | argchoice:Do not bootstrap:CONSFLAG=;protml $MODEL $SEARCH -v -I in1.in |
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| 17 | argchoice:10: arb_echo 1 r 10 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 10 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile |
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| 18 | argchoice:100: arb_echo 1 r 100 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 100 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile |
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| 19 | argchoice:1000: arb_echo 1 r 1000 y |seqboot ; /bin/mv -f outfile infile; arb_echo m 1000 y |$PROGRAM; /bin/mv -f treefile infile;arb_echo y | consense;arb_textedit outfile |
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| 20 | |
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| 21 | arg:MODEL |
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| 22 | argtype:chooser |
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| 23 | arglabel:Which model to use ? |
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| 24 | argchoice:JTT:-j |
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| 25 | argchoice:Dayhoff:-d |
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| 26 | argchoice:mtREV24:-m |
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| 27 | argchoice:Poisson:-p |
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| 28 | argchoice:Jones Tayler & Thornton:-jf |
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| 29 | argchoice:Dayhoff-F:-df |
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| 30 | argchoice:Adachi & Hasegawa(1995):-mf |
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| 31 | |
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| 32 | arg:SEARCH |
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| 33 | argtype:chooser |
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| 34 | arglabel:Search Strategie |
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| 35 | argchoice:star decomposition:-s |
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| 36 | argchoice:exhaustive:-e |
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| 37 | argchoice:quickadd:-q |
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| 38 | |
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| 39 | in:in1 |
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| 40 | informat:genbank |
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| 41 | inmask: |
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| 42 | insave: |
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