source: branches/lib/HELP_SOURCE/source/ne_align_seq.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
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_edit4.hlp
5#       sub topics:
6#SUB     subtopic.hlp
7SUB     pt_server.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Old aligner from ARB_EDIT
13
14OCCURRENCE      ARB_EDIT4/Edit/Old aligner from ARB_EDIT
15
16DESCRIPTION     Aligns or realigns selected sequence with the database
17                sequences. The most similar database sequences are
18                found, and the new sequence is aligned with these according to
19                primary and secondary structure similarity.
20
21                Select whether to align the sequence of the selected species or
22                all marked species.
23
24                Select whether to align versus an explicit reference or
25                the nearest relative reported by the PT_SERVER.
26
27                The used relatives may be marked by checking 'Mark sequences
28                found by the pt_server'.
29
30                Press <GO>
31
32NOTES           Marking the closest relatives allows manual optimization of the alignment
33                of the new species with its closest relatives.
34
35EXAMPLES        None
36
37WARNINGS        The aligner version available with the present package often
38                does not properly align short partial sequences.
39
40BUGS            The aligner needs lots of computer memory, sometimes more than
41                you have. In this case it may not align some sequences.
42
43                The aligner does not align the last 3-6 bases of short sequences
44                correctly. Look at the end of your sequences.
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