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# Calculate the Percentage of the Most Frequent Base

- OCCURRENCE
- DESCRIPTION
- NOTES
- EXAMPLES
- NOTES
- BUGS

## 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