You can modify the appearance of the MSA editor window. Controls for all multiple alignment preferences are grouped together in the Multiple Alignment Options dialog box, which you can access from the MSA Editor window by selecting the Preferences button.
In the Multiple Alignment Options dialog box, settings are organized into categories, accessed by selecting tabs at the top of the dialog box. The MSA Editor display options are set using its Editor and Consensus tabs.
(For information on the options for Text Display, Picture Fonts and Picture Shading, see the "Displaying multiple alignments" help topic.)
TO SET THE EDITOR options for the MSA editor window
1. Select the preferences button in the MSA editor window. The Multiple Alignment Options dialog box is displayed, with the Editor tab selected.
2. To control sequence numbering, do one of the following:
- select the None radio button if you do not want residue numbers to be displayed.
- select the Top radio button to display residue numbers across the top of the alignment; then use the text box to set the interval at which numbers will be displayed (default is 10).
3. Select the Outline Colors check box to display each residue with a dark outline, for greater contrast.
NOTE: Color mode must be enabled for this option to work. To toggle the color display on, select the color mode button in the MSA Editor window.
4. To allow regions of the aligned sequences to be excluded from phylogenetic recontruction analyses, select the Show Position Mask check box.
5. Select Apply to see the effects of your changes on any open MSA editor windows.
6. Select OK to save the changes and close the dialog box.
Alternatively, select Defaults to reset the default settings, or Cancel to close the dialog box without saving.