Calculates consensus for marked or all sequences.
-
Choose an 'alignment' (see ´Glossary´) from the
'Alignment' subwindow.
-
Define whether 'marked' (see ´Glossary´) or all
sequences should be used by pressing the respective
checkbox after the 'species' prompt.
-
Define whether to use or to ignore gaps entirely. If you count
gaps and the gap frequency exceeds 'threshold for gaps', the
result will be shown as '-'. If the switch is 'off',
the algorithm will virtually remove all gaps.
That means if you have a coloumn with two 'A's
and 500 gaps the program thinks
of 100% 'A'. If the switch would be 'on', the relative
number of 'A's would be 2%.
-
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.
The IUPAC codes are displayed after pressing the <show
IUPAC> button.
Characters are used for IUPAC encoding only if their
frequency exceeds 'threshold for character'.
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'.
-
Define a name for the consensus sequence by selecting one
from the 'SAI' subwindow or by typing it to the
'Name of New SAI' field.
|