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Last update on 04. Dec 2013 .
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Calculate the Percentage of the Most Frequent Base

OCCURRENCE

ARB_NT/SAI/create SAI/Max Frequency

 

DESCRIPTION

Finds the most frequent base in each column for all marked
species. Than the number of all sequences with this base are
divided by:
        a: the number of all marked sequences, if not ignoring gaps
        b: the number of bases in this column, if ignoring gaps
The resulting percentage is divided by ten and the second last
digit taken:

0%  - 25% will never occur
25% - 29% -> '2'
30% - 39% -> '3'
...
90% - 99% -> '9'
100%      -> '0'

 

NOTES

The result can be used as a conservation profile and filter: W.L.'s rule: The higher the number the more conserved the position.

 

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.

 

NOTES

'-' @#@ are regarded as gaps. '.' are always ignored.

 

BUGS

No bugs known yet