source: branches/lib/HELP_SOURCE/source/arb_pars_init.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: 1.2 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_pars.hlp
5#       sub topics:
6#SUB     subtopic.hlp
7
8# format described in ../help.readme
9
10
11TITLE           ARB PARSIMONY INTRO ( Filter Weights )
12
13OCCURRENCE      ARB_NT/Tree/Add Species to Tree
14
15DESCRIPTION     Set basic options for the parsimony program. If you do not want
16                to use a filter, you should select a filter (eg. E. coli) which excludes only
17                the big gaps in the alignment.  Otherwise the program will count
18                thousands of uninformative columns.
19                If you want a transversion parsimony, open the filter window,
20                and change the "simplify" option to TRANSVERSIONS ONLY
21
22NOTES           After pressing go, no species is added, no tree is changed,
23                you only get a new window (with some action buttons).   
24
25WARNINGS        You can only change filter settings at start-up time.
26                You should use filters in combination with large databases
27                to speed up computation.
28                Gaps ('-') are treated as bases, so check for gaps at
29                the beginning or end of short sequences. Replace them by
30                '.'.
31
32BUGS            All sequences are read at start-up time.  Sequence changes
33                afterwards are ignored.  Restart arb_parsimony if you want
34                them to take effect.
Note: See TracBrowser for help on using the repository browser.