source: trunk/HELP_SOURCE/source/compare_topo.hlp

Last change on this file was 19532, checked in by westram, 3 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: 1.2 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      treeadm.hlp
5
6#       sub topics:
7#SUB     subtopic.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Compare tree topologies
13
14OCCURRENCE      ARB_NT/Tree/Compare topology
15
16DESCRIPTION     Compares the topologies of the source and the destination tree.
17
18                For each subtree of the destination tree, the best matching subtree in the source
19                tree is searched.
20
21                If any source subtree contains the same set of species (while disregarding the
22                subtree topology itself), the destination subtree parent branch will not get
23                any annotation.
24
25                Otherwise the number of differences (i.e. the number of missing plus
26                additional species) to the best matching source subtree is written to
27                the destination subtree parent branch.
28
29NOTES           To remove the generated annotations use LINK{trm_boot.hlp}.
30
31SECTION         RELATED
32
33                To compare taxonomies use LINK{compare_taxonomy.hlp}.
34
35WARNINGS        Calling this function will delete existing bootstrap values from the destination tree.
36
37BUGS            far too slow :-(
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