source: branches/lib/HELP_SOURCE/source/nni.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: 1.3 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      pars.hlp
5UP      mode_kernlin.hlp
6UP      mode_optimize.hlp
7
8#       sub topics:
9#SUB     subtopic.hlp
10
11# format described in ../help.readme
12
13
14TITLE           NNI (Nearest Neighbour Interchange)
15
16DESCRIPTION     Searches for a better (more parsimonious) tree by swapping the
17                relative positions of subtrees separated by one edge.
18                At each inner edge (i.e. at non-leaf edges) three different
19                topologies are possible.
20
21                Testing these 3 possible topologies and keeping the best of them,
22                is called "Nearest Neighborhood Interchange" (NNI).
23
24SECTION         Possible topologies tested by NNI
25
26                The 3 different topologies checked by performing a NNI are
27
28                (A,B,C = subtrees; R = rest of tree)
29
30                        R           R           R
31                         \           \           \
32                         /\          /\          /\
33                        A  \        B  \        C  \
34                           /\          /\          /\
35                          B  C        A  C        B  A
36
37
38                Note: there are no other possible topologies containing A,B,C and R!
39
40WARNINGS        None
41
42BUGS            No bugs known
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