source: trunk/HELP_SOURCE/source/consensus_def.hlp

Last change on this file was 19532, checked in by westram, 3 months ago
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Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6
7# format described in ../help.readme
8
9
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                     Define whether to use or to ignore gaps entirely:
18
19                            If you count gaps and the gap frequency exceeds the specified
20                            threshold, the consensus will show a '-'.
21
22                            If the switch is 'off', the algorithm will virtually remove all gaps.
23                            That means if you have a column with 10 'A's
24                            and 500 gaps the program thinks of 100% 'A'
25                            (if the switch is 'on', the relative number of 'A's would be 2%).
26
27                     Regardless of how gaps are handled,
28                     if a column contains only gaps, the consensus will always show a '='.
29
30                Simplify using base character groups
31
32                     If grouping is 'off' the most frequent character will be used in consensus (even
33                     if another character has the same frequency).
34
35                     If grouping is 'on' base characters will be grouped as follows:
36
37                        * RNA/DNA alignments use the IUPAC ambiguity codes (MRWSYKVHDBN)
38                        * Amino acid alignments use amino acid classes (ADHIFC)
39
40                     Click the "Show IUPAC" button to display detailed information
41                     about these character groups.
42
43                     The threshold defines how characters are grouped:
44
45                        * in RNA/DNA alignments the threshold specifies, whether a
46                          non-ambiguous character is considered for grouping (i.e.
47                          all characters below the threshold will be removed and the
48                          rest will be grouped. See also example below)
49
50                        * in amino acid alignments the threshold specifies, whether
51                          all characters of a group together are frequent enough to
52                          show that group in the consensus. If not, an 'X' will be displayed
53                          in consensus.
54
55                     Example:
56
57                        If you have 40% 'A', 10% 'C', 40% 'G' and 10% 'T' and
58                        'threshold for character' is set to 20%, arb will
59                        use the iupac code representing 'A' and 'G' (i.e. 'R').
60
61                     Reasonable thresholds explained:
62
63                        * amino acid:
64                          * 51% means: if most belong to one amino acid group, then show it (otherwise show 'X')
65                        * RNA/DNA:
66                          * 26% means: group up to 3 nucleotides in an ambiguity code (otherwise show most frequent base)
67                          * 25% means: group up to 4 nucleotides, i.e. will produce 'N' in consensus (only if the nucleotides are distributed EXACTLY even)
68                          * 20% is similar to 25%, but also slightly uneven distributions will produce 'N'
69                          * 51% will effectively turn off IUPAC grouping for nucleotides
70                          * 50% will group 2 nucleotides (only if they are distributed EXACTLY even)
71                          * 33% will group up to 3 nucleotides (only if they are distributed EXACTLY even)
72
73                Show as upper or lower case?
74
75                     Define whether the character is displayed in upper or lower case
76                     or whether a dot is displayed.
77
78                     Define upper and lower limit:
79
80                            If the percentage of a character is above or equal to the upper
81                            limit, the character is displayed in upper case.
82
83                            If the percentage of a character is above or equal to the lower
84                            limit and below the upper limit, the character is displayed in lower case.
85
86                            Otherwise a dot ('.') is displayed.
87
88                     If gaps are ignored (as explained at top), the percentage is calculated relative
89                     to all existing bases in the column.
90                     If gaps are NOT ignored, the percentage is calculated relative to the number of species.
91
92NOTES           You can save/load the consensus settings to/from a file using the config-manager icon.
93                This allows you to exchange
94                     * the consensus settings used in EDIT4 and
95                     * the settings used to calculate the SAI 'CONSENSUS' from the ARB main window.
96
97EXAMPLES        None
98
99WARNINGS        None
100
101BUGS            None
102
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