source: branches/lib/HELP_SOURCE/source/pa_add.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: 1.4 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6#SUB     subtopic.hlp
7
8# format described in ../help.readme
9
10
11TITLE           Add species with local optimization
12
13OCCURRENCE      ARB_PARSIMONY/Tree/Add Species to Tree/Add Marked Species + Local Optimization (NNI)
14                ARB_PARSIMONY/Tree/Add Species to Tree/Add Selected Species + Local Optimization (NNI)
15                ARB_PARSIMONY/Tree/Add Species to Tree/Remove & Add Marked + Local Optimization (NNI)
16
17DESCRIPTION     The functions work like their counterparts described in LINK{pa_quick.hlp}.
18
19                Additionally after all species have been inserted, a LINK{pa_locopti.hlp} takes place.
20                This optimization operates on all branches to subtrees containing marked species
21                and does not stop at folded groups - regardless
22                which settings are selected in LINK{pa_optimizer.hlp}.
23
24WARNINGS        That local optimization will not avoid the need for global tree
25                optimization (see LINK{pa_globopti.hlp}).
26
27                Using this function for a bigger number of species (or repeatedly using it), will
28                cause your tree to degenerate (see section 'Tree degeneration' in LINK{pa_quick.hlp}
29                for more information. What is said there also applies here, the effects are just less worse here).
30
31NOTES           None
32
33EXAMPLES        None
34
35BUGS            No bugs known
Note: See TracBrowser for help on using the repository browser.