The Multiple Alignment Text view displays the alignments in a text view. Under the alignment is an identity line, which indicates using symbols where there are identities and similarities in the alignment. The window includes a custom header that displays additional parameters and scores for the alignment.
The text multiple alignment can be exported as a text file.
TO DISPLAY the Multiple Alignment Text window
1. In the Text Display panel of the Alignment Views dialog box, select the Multiple Alignment check box.
2. Select OK to generate the display window.
NOTE: You can generate any combination of the results windows at one time by setting the required options before selecting OK.
The appearance of the Multiple Alignment Text window can be modified in a number of ways.
TO MODIFY the Multiple Alignment Text window
1. Do one of the following:
- In the MSA Editor window, select the Preferences button
- In the Alignment Views dialog box, select Set Options.
The Multiple Alignment Options dialog box is displayed.
2. Select the Text Display tab.
3. If you want to show identical residues in the identity line, select the Show identities check box, and then choose the required Identities marker from the radio button and text box options.
4. If you want to show similar residues in the identity line, select the Show similarities check box, and then choose the required Similarities marker from the radio button and text box options.
5. If you want to stop the ends of aligned sequences from being padded with the "-" symbol, select the Suppress "-" at ends check box.
6. Enter the number of residues per line in the Line length text box.
7. Choose a numbering style for the alignments, by selecting one of the Numbering radio buttons.
8. Select Apply to see the effects of your changes on any open MSA editor windows.
9. 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.
Displaying multiple alignments