|
Last change
on this file was
11886,
checked in by westram, 12 years ago
|
- reintegrates 'cleanup' into 'trunk'
- adds:
|
-
Property svn:eol-style set to
native
-
Property svn:keywords set to
Author Date Id Revision
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|
File size:
1.1 KB
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| Line | |
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| 1 | item:Positional Variability by Olsons dnamlrates (max 5000 Species, 8000 seqlength) |
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| 2 | seqtype: N |
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| 3 | itemmeta: O |
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| 4 | itemmethod:(GOTO_LOCAL_DIR ; \ |
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| 5 | arb_export_rates --arb-notify "" "M $RESIDUES" "T $TTRATIO" "U" $LENGTHS "F" | GEN_FASTDNAML(dnarates.in) && \ |
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| 6 | ( echo 1; arb_export_tree $TREE || STOP_ON_FAILURE(arb_export_tree '$TREE') ) >>dnarates.in && \ |
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| 7 | RUN_IN_WINDOW(arb_dnarates dnarates.in); \ |
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| 8 | RM_LOCAL_FILES(TmpInputFile dnarates.in) )& |
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| 9 | |
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| 10 | itemhelp:DNAml_rates.help |
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| 11 | |
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| 12 | arg:TREE |
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| 13 | argtype:tree |
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| 14 | arglabel:Base Tree |
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| 15 | argchoice:tree_main |
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| 16 | |
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| 17 | arg:RESIDUES |
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| 18 | argtype:text |
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| 19 | arglabel:Number of informative residues |
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| 20 | argtext:10 |
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| 21 | |
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| 22 | arg:TTRATIO |
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| 23 | argtype:text |
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| 24 | arglabel:Transition/transversion ratio |
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| 25 | argtext:2.0 |
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| 26 | |
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| 27 | arg:LENGTHS |
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| 28 | argtype:choice_menu |
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| 29 | arglabel:Use branchlengths? |
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| 30 | argchoice:Yes:"L" |
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| 31 | argchoice:No: |
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| 32 | |
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| 33 | // arg:USERRATES |
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| 34 | // argtype:text(20) |
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| 35 | // arglabel:User frequency rates |
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| 36 | // argtext:F |
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| 37 | |
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| 38 | // arg:USERRATES |
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| 39 | // argtype:choice_menu |
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| 40 | // arglabel:Choose frequency rates |
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| 41 | // argchoice:Calculate frequencies:F |
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| 42 | // argchoice:Estimate equal frequencies:F 0.25 0.25 0.25 0.25 |
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| 43 | |
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| 44 | in:TmpInputFile |
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| 45 | informat:genbank |
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| 46 | insave: |
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