source: branches/lib/HELP_SOURCE/source/pa_kernlin.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: 1.6 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      pars.hlp
5UP      mode_nni.hlp
6UP      mode_optimize.hlp
7
8#       sub topics:
9#SUB     subtopic.hlp
10
11# format described in ../help.readme
12
13
14TITLE           K.L. optimization
15
16OCCURRENCE      ARB_PARSIMONY/<K.L.-mode-button>
17                as part of LINK{pa_globopti.hlp}
18
19DESCRIPTION     Searches for a better (more parsimonious) tree by swapping
20                subtrees which are separated by many edges.
21
22                Not all possible topologies are tested here, because there
23                are far too many (see LINK{kernlin.hlp} for details).
24
25                Instead the K.L. optimizer selects several "paths" through the tree (we call
26                this selection 'path reduction') and follows only those paths, while performing
27                NNIs (see LINK{nni.hlp}) along it's way.
28
29                These NNIs are even attempted, when single NNIs degrade the quality of the topology.
30                If some intermediate or the final NNI (which is by default done 15 edges away from
31                the edge starting from) leads to an improvement of the tree, the topology change
32                is kept. Otherwise all changes are undone and the next path will be attempted.
33
34                The default maximum path length of 15 and several parameters concerning the path reduction
35                may be configured in LINK{kernlin.hlp}.
36
37NOTES           The K.L. optimization occurs as step 2 of LINK{pa_globopti.hlp}.
38
39                It can be called directly using LINK{mode_kernlin.hlp}.
40
41EXAMPLES        None
42
43WARNINGS        None
44
45BUGS            No bugs known
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