source: branches/tree/HELP_SOURCE/source/max_freq.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE           Calculate the Percentage of the Most Frequent Base

OCCURRENCE      ARB_NT/SAI/create SAI/Max Frequency

DESCRIPTION     Finds the most frequent base (or gap) in each column for all marked
                species. Then the number of all sequences with this base are
                divided by:

                        * the number of all marked sequences (if not ignoring gaps)
                        * the number of bases in this column (if ignoring gaps)

                The resulting percentage is divided by ten and then the second last
                digit is taken:

                        0%  - 19%  ->  '1' (does not occur for nucleotides)
                        20% - 29%  ->  '2'
                        30% - 39%  ->  '3'
                        ...
                        90% - 99%  ->  '9'
                        100%       ->  '0'


NOTE            The result can be used as a conservation profile and filter.
                Rule of thumb:
                the higher the number, the more conserved the position (but mind the '0' which means 100%!).

                Internally the SAI consists of two lines: the main line called 'data' and a second line called 'dat2'.

                  The first is used when you use the SAI as conservation profile or filter and
                  contains the SECOND LAST digit of the calculated frequencies.

                  The second contains the LAST digit of the calculated frequencies. It is not used and does only
                  show up, when you load the SAI into ARB_EDIT4, where it will show both lines.

EXAMPLES        Say one column contains 7 A's 4 G's and 5 Gaps.

                 * ignoring gaps will result in 7/11 == 64 % which is converted to '6'.
                 * otherwise we get 7/16 == 44% which will be indicated by a '4' in the target sequence.

SECTION         Gaps

                If gaps are ignored '-' are treated like '.': both get removed and frequency is calculated on non-gaps only.

                If gaps are NOT ignored, '-' are treated like non-gaps, i.e. a column containing only '-' will be assigned a
                max. frequency of 100%. '.' are treated as gaps.

SECTION         Ambiguities

                Ambiguities are counted proportionally, i.e.

                  * a 'N' counts as 1/4 'A', 1/4 'C', 1/4 'G' and 1/4 'T'
                  * a 'D' counts as 1/3 'A', 1/3 'G' and 1/3 'T'
                  * a 'Y' counts as 1/2 'C' and 1/2 'T'

                Example:

                        A column containing 9 'C' and one 'Y' results in a max. frequency of 95% (=9.5 'C').

BUGS            No bugs known yet