source: branches/lib/HELP_SOURCE/source/arb_pars.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug 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
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.3 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6SUB     mode.hlp
7SUB     arb_pars_init.hlp
8SUB     ap_stack.hlp
9
10# format described in ../help.readme
11
12
13
14TITLE           ARB Parsimony
15
16OCCURRENCE      ARB_NT/Tree/Add species to existing tree/Parsimony ...
17
18DESCRIPTION     The 'ARB_Parsimony' and 'ARB_NT' windows are similar. 'ARB_
19                Parsimony' contains a subset of 'ARB_NT' functions and in
20                addition some tools for tree reconstruction and evaluation.
21
22        Clicking on the prompts in the horizontal menu bar in the upper part of
23        the window displays the corresponding submenus. The submenus are
24        also available using keyboard shortcuts by pressing the meta and
25        a letter key indicated in the main menu bar by underlining.
26
27        The elements in the area between the main menu bar and the tree display
28        area ('top area') from left to right:
29
30                * Tree button: Displays the name of the current tree.
31                * Stack button: Displays the number of currently stored tree topologies (see LINK{ap_stack.hlp}).
32                * Current parsimony value: Displays the parsimony value of the
33                  current topology (see LINK{pa_value.hlp}).
34                * Jump button: Centers the currently LINK{selected.hlp}.
35                * HELP button: Displays this help information.
36
37         Second row
38
39                * Radial tree display
40                * Dendrogram tree display
41                * RESTORE: restores previously stored topology
42                * STORE: stores the current topology for later restore
43                * Optimal parsimony value: Displays the best so far encountered parsimony value (see LINK{pa_reset.hlp}).
44
45        Main functions:
46
47        * quick adding species (see LINK{pa_quick.hlp})
48        * add species with local optimization (see LINK{pa_add.hlp})
49        * topology optimization (see LINK{pa_optimizer.hlp})
50
51
52NOTES           ARB_PARSIMONY is not designed to CREATE trees from scratch.
53                To do this you have to create a base tree containing at least 2 species
54                using some other program (e.g. LINK{dist.hlp}).
55
56WARNINGS        ARB_PARSIMONY works on the selected tree, it does instantly change the database.
57
58EXAMPLES        None
59
60BUGS            None
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