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Last change
on this file was
19532,
checked in by westram, 4 months ago
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- reintegrates 'help' into 'trunk'
- tweak arb documentation:
- automatically link
- ticket references to arb
 tracker (only affects html version).
- found URLs.
- page titles
- warn about long titles.
- introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
- increase allowed length (limited by subwindow width).
- cleanup header sections in all helpfiles.
- fix and/or update several help files.
- document syntax of help sources.
- build issues:
- when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
- remove output files on error (including files below ARBHOME/lib).
- pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
- moves Tree admin + NDS menu entries to top of menu
- adds: log:branches/help@18783:19531
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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:
930 bytes
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| 1 | # main topics: |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | |
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| 5 | # sub topics: |
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| 6 | |
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| 7 | # format described in ../help.readme |
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| 8 | |
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| 9 | |
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| 10 | TITLE Trees |
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| 11 | |
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| 12 | OCCURRENCE ARB_NT |
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| 13 | |
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| 14 | DESCRIPTION A tree consists of two types of 'nodes': |
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| 15 | |
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| 16 | - tips or terminal nodes: species |
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| 17 | |
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| 18 | connected to exactly one father |
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| 19 | |
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| 20 | - inner nodes: hypothetical ancestors |
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| 21 | |
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| 22 | connected to one father |
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| 23 | (and in the binary case to two children). |
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| 24 | A group_name may be assigned to an inner node; in this |
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| 25 | case, the node and all its children become a group. |
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| 26 | <ARB_NT/INFO_MODE/M> |
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| 27 | |
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| 28 | There are significant differences between |
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| 29 | phylogenetic trees and binary trees: |
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| 30 | |
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| 31 | phylogenetic trees binary trees: |
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| 32 | ------------------------------------------------------------------------- |
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| 33 | unrooted rooted |
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| 34 | inner nodes have n children all inner nodes have two children |
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| 35 | |
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| 36 | Since binary trees are much easier to handle, ARB converts |
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| 37 | phylogenetic trees to binary trees. |
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| 38 | |
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