source: branches/lib/HELP_SOURCE/source/st_ml.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: 2.8 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           Column Statistic (Prototype)
12
13OCCURRENCE      ARB_EDIT4/View/Activate column statistics
14                ARB_EDIT4/View/Disable column statistics
15                ARB_EDIT4/View/Toggle detailed Col.-Stat.
16                ARB_EDIT4/View/Set threshold for D.c.s.
17
18DESCRIPTION     Highlights unlikely bases in an alignment using the maximum
19                likelihood technique.
20
21                As soon as the go button is pressed, the tree selected in ARB_NT
22                and all marked sequences are read. Then the relative
23                likelihood for each base is calculated and transformed to
24                a number between 0 and 9. This number is translated into a color,
25                using the colors 'RANGE 0 ... RANGE 9'. The higher the number,
26                the more unlikely a particular base.
27
28                You may improve the output by selecting a valid column statistic,
29                which holds information about column dependent rates and base
30                frequencies.
31
32NOTES           To change the colors used for column statistics,
33                edit "RANGE 0" up to "RANGE 9" in LINK{color_props.hlp}.
34
35                All sequences that should be analyzed, have to be marked and
36                have to be members of the tree currently shown in the ARB main window!
37                The program assumes that your tree has good quality - if it does
38                not, results may be quite useless.
39
40                See also LINK{e4_background_priority.hlp}.
41
42WARNINGS        This is only a prototype, don't expect something perfect.
43
44                Without a powerful computer only a small number of sequences can
45                be viewed.
46
47BUGS            The program can only be started once.
48
49SECTION         Detailed column statistic
50
51                This special mode displays 4 rows below the sequence containing
52                the likelihood of each base character.
53
54                Each row consists of two rows of digits displayed in the same color
55                (which actually is the color normally used for displaying the
56                appropriate base character). The upper of these two rows is the
57                first, the lower the second digit of the likelihood.
58                [You may like to use the cursor to simplify reading]
59
60                Special character used:
61                -----------------------
62                SPACE   = likelihood is 20%
63                ^       = likelihood is 100%
64                ?       = can't determine likelihood for that column
65
66                Background colors used:
67                -----------------------
68                Normally the normal background color is used.
69
70                If a column has a significant likelihood for one base character
71                (or for the sum of two base characters), all four rows are
72                displayed in color 'Range 0'.
73
74                [significance is 90% (hardcoded) - will be made utilizable soon]
75
76                The single (or two) base character(s) responsive for the
77                significance will be displayed in colors 'Range 1' to 'Range 8'
78                (the higher the Range-number is, the higher is the likelihood)
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