source: branches/lib/HELP_SOURCE/source/syncroots.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
File size: 2.1 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6SUB     mode_setroot.hlp
7
8# format described in ../help.readme
9
10
11TITLE           Auto-adjust roots of trees
12
13OCCURRENCE      ARB_NT/Tree/Adjust roots
14
15DESCRIPTION     This module allows to synchronize the root position of single or
16                multiple tree topologies.
17
18                It provides two different methods:
19
20                * adjust roots of one (or several) trees versus one
21                  reference tree.
22                * optimize root positions of multiple trees at once
23                  to find the minimum combination of pairwise distances.
24
25                Use the buttons between the two selection lists
26                to move the trees which should be optimized into the left list.
27
28                Select the wanted reference tree in the right list and
29                press the button at the bottom right to adjust the roots of
30                all chosen trees versus the reference tree.
31
32                To optimize the root combination of all chosen trees, press the
33                lower left button.
34                This starts a heuristic which tries to find better roots for all
35                selected trees, such that the overall sum of pairwise differences
36                gets minimal.
37
38                Opposed to the first method (using a reference tree) the second approach
39                may not necessarily find an optimal distribution of root nodes.
40                Its result may depend on the root positions of the involved trees at startup
41                and therfore using the first method before the second may improve the found result.
42                This method also optimizes the root positions of all trees towards "the center"
43                of all involved species.
44
45NOTES           Pressing abort when optimizing root positions of multiple trees, will
46                keep the best so far found positions.
47
48EXAMPLES        None
49
50WARNINGS        Be aware that changing the position of the trees root does affect the
51                orientation of taxonomic groups.
52                For details refer to LINK{keeled_groups.hlp}.
53
54BUGS            No bugs known
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