source: branches/species/HELP_SOURCE/source/mg_preserve.hlp

Last change on this file was 19532, checked in by westram, 7 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: 2.4 KB
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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           Alignment adaption (select species)
12
13                Select species to use for alignment adaption
14
15OCCURRENCE      ARB_MERGE/TRANSFER SPECIES (Adapt alignment/SELECT)
16
17DESCRIPTION     Helps you finding candidates for alignment preservation.
18
19                Normally people have inserted new gaps in one of the two databases.
20                ARB Merge tries to adapt the alignment.
21
22                To be able to do this, you have to specify one or more species or SAIs
23                existing in BOTH databases. ARB Merge then creates a column reference list
24                and realigns all transferred species according to this list.
25
26                Press the 'Find candidates' button to search both databases for candidate
27                species/SAIs and rate them.
28
29                A list of species/SAIs shows up. The first column contains the name,
30                the second column the number of alignments containing data for this species/SAI,
31                the third column shows the position-count-difference (see below),
32                the fourth column is the score (higher value means better).
33
34                The list is sorted by score, i.e. best candidates are listed at the top.
35
36                The term 'position-count-difference' is calculated like follows:
37                For all alignments the number of non-gaps (i.e. neither '-' nor '.') are counted and
38                the differences between these counts are summarized for all alignments.
39                Best value is 0, which normally means the sequence data of the species (or the SAI data)
40                didn't change. A high value means that species changed data and isn't a good candidate
41                for alignment preservation.
42
43                To enable this feature, enable the 'Adapt alignment' toggle.
44
45NOTES           In our database releases we provide SAIs named 'gaps_...'.
46                These SAIs are the best candidates for alignment preservation.
47
48                When merging similar databases with many species, searching adapt candidates
49                may take a long time. Press KILL in the status window to abort the process.
50
51EXAMPLES        None
52
53WARNINGS        Calculated SAIs (like MAX_FREQUENCY or POS_VAR_BY_PARSIMONY) show up on top
54                but they are normally NO good candidates for preservation.
55
56BUGS            No bugs known
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