Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...

The Total button, on the bottom left of the table, sorts the sample columns so that the
samples with the greatest number of differences move to the left. Click Total again, and
the columns sort in the opposite order.
There are two ways to define the sort order for the rows. You can sort by total number of
differences or you can sort by 5’-3’order. In the default, unsorted display of the Variance
Table, rows are sorted by base position in ascending (5’- 3’) order. When you click on
Total in the top right corner of the Variance Table, the rows are rearranged so that those
with the greatest number of differences sort to the top. Click the Total button again to
reverse the order.
To restore the order by base position, click on the button in the top left corner of the
Variance Table. Click here again to have the rows sort by position in descending (3’-5’)
order.
Note: The text on the sort button is context sensitive and will change depending on the
Compare Bases To command used to generate the Variance Table.
Removing columns from the Variance Table
As you start to work with your Variance Table you may decide that some sequences are
no longer of interest. The Edit menu’s Remove From Table command allows you to
delete sequences selectively from your Variance Table.
To select a continuous range of sequences, choose the first sequence by clicking on its
column header and then, holding down the Shift key, select the last sequence in the same
fashion. To select a discontinuous list of sequences, hold down the Control key while
clicking on the sequences. Go to the Edit menu and choose the Remove From Table
command.
Note: The Remove From Table command does not remove sequences from the
underlying contig.
Review Mode
In Review mode, the Variance Table lets you view the data supporting each cell (see
Figure 13-15). You can access the Review Mode by clicking on the Review button in the
Variance Table button bar or by double clicking on any cell in the table. Sequencher will
open both the Contig and Chromatogram editors with the associated base or column of
bases selected.
You can specify the layout of these three Review windows, the Variance Table, the Contig
Editor, and the Contig Chromatogram Editor, and then set the new organization as your
default layout. After you have arranged your windows, go to the Window menu and
choose the Remember Window Layout command, then select Single Variance Table
Review from the submenu.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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