source: branches/lib/HELP_SOURCE/source/pa_optimizer.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: 2.1 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_pars.hlp
5
6#       sub topics:
7#SUB     subtopic.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Tree optimization
13
14OCCURRENCE      ARB_PARSIMONY/Tree/Tree Optimization
15
16DESCRIPTION     This subwindow allows you to configure and access
17                LINK{pa_locopti.hlp}, LINK{pa_globopti.hlp} and LINK{pa_mixtree.hlp}.
18
19                First you can select whether these functions are applied to the whole tree or
20                whether they only operate on subtrees containing marked species and/or they
21                only operate on visible (i.e. unfolded) parts of the tree.
22
23                Note:
24
25                    The default behavior until arb-7.0 was to operate on marked and visible parts
26                    only. Due to several, now fixed bugs it did not strictly restrict to these parts
27                    while optimizing.
28
29                Then you may trigger the wanted optimization/randomization using the following buttons:
30
31                * 'Recursive NNI' will trigger LINK{pa_locopti.hlp}
32                * 'Heuristic optimizer' will trigger LINK{pa_globopti.hlp}
33                * 'Randomize tree' will trigger LINK{pa_mixtree.hlp}
34
35                For the 'Heuristic optimizer' click 'Settings' to change LINK{kernlin.hlp}.
36
37NOTES           When only optimizing subtrees with marked species, only branches that are drawn in
38                'Marked' or 'Some marked' color will be modified.
39
40                The tree optimizations may as well be called using the 3 tree-modes LINK{mode_nni.hlp},
41                LINK{mode_kernlin.hlp} and LINK{mode_optimize.hlp}. Opposed to using the buttons in
42                the 'Tree optimization' window, these modes normally operate on the clicked subtree only.
43
44                After any optimization/randomization the tree will be 'beautified' (see
45                LINK{resorttree.hlp}) and branchlengths will be re-calculated (see LINK{pa_branchlengths.hlp}).
46
47                Saving the current settings as configuration will save the properties from this window
48                and from the LINK{kernlin.hlp} window.
49
50EXAMPLES        None
51
52WARNINGS        None
53
54BUGS            No bugs known
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