source: branches/profile/HELP_SOURCE/oldhelp/consensus_def.hlp

Last change on this file was 6141, checked in by westram, 16 years ago
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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4
5#Please insert subtopic references  (line starts with keyword SUB)
6
7# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
8
9#************* Title of helpfile !! and start of real helpfile ********
10TITLE           How is the consensus calculated?
11
12OCCURRENCE      ARB_NT/SAI/Create SAI using../Consensus
13                ARB_EDIT4/Properties/Consensus definition
14
15DESCRIPTION     What to do with gaps?
16
17                     If a column contains only gaps the result will be shown as '='.
18
19                     Define whether to use or to ignore gaps entirely:
20
21                            If you count gaps and the gap frequency exceeds 'threshold for gaps',
22                            the result will be shown as '-'.
23
24                            If the switch is 'off', the algorithm will virtually remove all gaps.
25                            That means if you have a column with two 'A's
26                            and 500 gaps the program thinks of 100% 'A'.
27                            (If the switch is 'on', the relative number of 'A's would be 2%)
28
29                Simplify using IUPAC
30
31                     Define whether the most frequent base or the IUPAC code
32                     (more then one base) should be shown at the particular
33                     position by pressing the respective checkbox after the
34                     'simplify' prompt.
35
36                     Characters are used for IUPAC encoding only if their
37                     frequency exceeds 'threshold for character'.
38
39                     Example:
40
41                        If you have 40% 'A', 10% 'C', 40% 'G' and 10% 'T' and
42                        'threshold for character' is set to 20%, the
43                        program looks for a iupac code only for 'A' and 'G'.
44
45                     Note:
46
47                        The IUPAC codes are displayed after pressing
48                        the 'show IUPAC' button.
49
50                Show as upper or lower case?
51
52                     Define whether the character is displayed in upper or lower case
53                     or whether a dot is displayed.
54
55                     Define upper and lower limit:
56
57                            If the percentage of a character is above or equal to the upper
58                            limit, the character is displayed in upper case.
59
60                            If the percentage of a character is above or equal to the lower
61                            limit and below the upper limit, the character is displayed in lower case.
62
63                            Otherwise a dot ('.') is displayed.
64
65NOTES           None
66
67EXAMPLES        None
68
69WARNINGS        IUPAC symbols in source sequences are ignored.
70
71BUGS            'LINK{consensus.ps}' is broken for more than 10 years
72                now. Seems that nobody ever took a look.
73
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