What to do with gaps?
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If a column contains only gaps the result will be shown as '='.
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Define whether to use or to ignore gaps entirely:
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If you count gaps and the gap frequency exceeds 'threshold for gaps',
the result will be shown as '-'.
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If the switch is 'off', the algorithm will virtually remove all gaps.
That means if you have a column with two 'A's
and 500 gaps the program thinks of 100% 'A'.
(If the switch is 'on', the relative number of 'A's would be 2%)
Simplify using IUPAC
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Define whether the most frequent base or the IUPAC code
(more then one base) should be shown at the particular
position by pressing the respective checkbox after the
'simplify' prompt.
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Characters are used for IUPAC encoding only if their
frequency exceeds 'threshold for character'.
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Example:
If you have 40% 'A', 10% 'C', 40% 'G' and 10% 'T' and
'threshold for character' is set to 20%, the
program looks for a iupac code only for 'A' and 'G'.
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Note:
The IUPAC codes are displayed after pressing
the 'show IUPAC' button.
Show as upper or lower case?
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Define whether the character is displayed in upper or lower case
or whether a dot is displayed.
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Define upper and lower limit:
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If the percentage of a character is above or equal to the upper
limit, the character is displayed in upper case.
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If the percentage of a character is above or equal to the lower
limit and below the upper limit, the character is displayed in lower case.
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Otherwise a dot ('.') is displayed.
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