| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | UP treeadm.hlp |
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| 5 | |
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| 6 | #Please insert subtopic references (line starts with keyword SUB) |
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| 7 | #SUB subtopic.hlp |
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| 8 | |
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| 9 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 10 | |
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| 11 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 12 | TITLE Export tree to file |
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| 13 | |
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| 14 | OCCURRENCE ARB_NT/Tree admin/Export |
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| 15 | |
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| 16 | DESCRIPTION Writes a tree to file in Newick format |
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| 17 | |
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| 18 | Press the 'EXPORT' button to display the 'TREE SAVE' window. |
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| 19 | |
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| 20 | Select a tree file from the 'Directories and Files' subwindow or |
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| 21 | type the file name to the 'FILE NAME' subwindow. |
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| 22 | |
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| 23 | NEWICK TREE FORMAT |
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| 24 | |
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| 25 | Nodetype |
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| 26 | |
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| 27 | Species ID |
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| 28 | |
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| 29 | This is the traditional format using species IDs as leaf names. |
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| 30 | |
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| 31 | NDS |
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| 32 | |
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| 33 | This uses the current NDS tree settings as leaf names, |
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| 34 | i.e. this mode can be used for EXPORT ONLY! |
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| 35 | (until #774 gets implemented). |
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| 36 | |
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| 37 | The "truncated" NDS mode respects the WIDTH entry in LINK{props_nds.hlp}, |
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| 38 | as done by the arb tree display. |
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| 39 | This was the hardcoded behavior until arb-7.0. |
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| 40 | |
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| 41 | The newer "untruncated" NDS mode ignores the WIDTH field and |
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| 42 | always exports complete field contents. |
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| 43 | |
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| 44 | Group names are now as well generated via NDS in NDS mode. |
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| 45 | To export plain group names, use a group NDS with WIDTH=0 and |
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| 46 | ACI='taxonomy(1)' (which is the current default). |
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| 47 | |
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| 48 | Label quoting |
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| 49 | |
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| 50 | choose whether and how to quote names for leafs and/or groups. |
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| 51 | Quoting names may be necessary to ensure other software is able |
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| 52 | to read the generated tree files. |
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| 53 | |
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| 54 | Replace problem chars |
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| 55 | |
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| 56 | if checked, problematic characters in labels will be replaced (currently "()[]:;," plus |
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| 57 | used quote, if any). |
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| 58 | |
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| 59 | Save group names |
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| 60 | |
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| 61 | if marked, groupnames (taxonomy) are written to the tree file. |
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| 62 | |
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| 63 | Save branch lengths |
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| 64 | |
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| 65 | if marked, branchlengths are written to the tree file. |
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| 66 | |
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| 67 | Save bootstraps |
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| 68 | |
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| 69 | if marked, bootstraps are written to the tree file. |
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| 70 | |
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| 71 | ARB_XML TREE FORMAT |
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| 72 | |
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| 73 | Simple XML Format (export only; experimental) |
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| 74 | |
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| 75 | Hide folded groups |
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| 76 | |
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| 77 | If checked, folded groups will be exported as terminal node. Otherwise |
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| 78 | group contents will be written into tree file. |
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| 79 | |
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| 80 | |
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| 81 | NOTES If you select both 'Save group names' and 'Save bootstraps', other programs may be |
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| 82 | unable to load the tree or at least unable to interpret the bootstrap values correctly. |
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| 83 | |
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| 84 | If a suffix is displayed in or typed to the 'SUFFIX' subwindow, |
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| 85 | only the corresponding filenames will be displayed. |
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| 86 | The suffix is automatically appended to the filename typed |
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| 87 | to the 'File Name' subwindow. |
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| 88 | |
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| 89 | The different export types cause the suffix to change: |
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| 90 | |
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| 91 | - '.tree' for normal newick |
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| 92 | - '.ntree' for newick using NDS |
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| 93 | - '.xml' for xml |
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| 94 | |
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| 95 | SECTION Keeled groups |
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| 96 | |
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| 97 | ARB will refuse to store LINK{keeled_groups.hlp} into a newick file. |
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| 98 | |
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| 99 | To work around that restriction either |
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| 100 | - uncheck 'Save group names' or |
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| 101 | - read about howto fix keeled groups. |
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| 102 | |
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| 103 | WARNINGS Tree data written with the 'NDS' option cannot be |
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| 104 | reimported to the database without data loss! |
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| 105 | |
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| 106 | It's possible to reload such a tree, but it's leafs |
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| 107 | will not be linked to the correct species. |
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| 108 | |
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| 109 | BUGS No bugs known |
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