source: branches/lib/HELP_SOURCE/source/pars.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: 1.8 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_pars.hlp
5
6#       sub topics:
7SUB     phylo.hlp
8
9# format described in ../help.readme
10
11
12
13TITLE           Starting ARB Parsimony
14
15OCCURRENCE      ARB_NT/Tree/Add species to existing tree/Parsimony ...
16
17DESCRIPTION     ARB Parsimony cannot be used to completely reconstruct new trees.
18
19                Existing trees can be optimized at different levels (depths)
20                according to maximum parsimony criteria.
21
22                New sequences (species) can be placed rapidly into an existing
23                tree. This can be done without changing that tree or allowing
24                optimization at different levels according to maximum parsimony
25                criteria including the new information for calculation.
26
27                    The different ways to add species are explained in LINK{pa_quick.hlp}.
28                    Standard 'quick add' is available in this menu. To customize behavior
29                    or to optimize trees you have to start ARB parsimony in interactive mode.
30
31                Filters for the in- or exclusion of alignment columns
32                ('ARB_NT/SAI; ARB_NT/Tree/Dist Matrix) can be selected.
33
34                After selecting one of the parsimony items in 'Tree/Add species to existing tree'
35                the 'SET PARSIMONY OPTIONS' window appears:
36
37                - Select the tree (to be modified) from the 'Tree:' subwindow.
38
39                - Select an 'alignment' (see LINK{glossary.hlp}) from the
40                  'alignment:' subwindow.
41
42                - To select a filter display the 'Select Filter' window pressing
43                  the button after the 'Filter:' prompt (see LINK{sel_fil.hlp}).
44
45                - Press the <GO> button to display the 'ARB_PARSIMONY' window.
46
47NOTES           ARB Parsimony will modify the given tree. It might be a good idea to
48                create a copy of your tree before you start doing so (see LINK{treeadm.hlp}).
49
50EXAMPLES        None
51
52WARNINGS        None
53
54BUGS            No bugs known
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