To control the ordering and naming of sequences, use the sequence name buttons in the panel to the left of the displayed residues.
CHANGING THE sequence display order
You can change the order in which the sequences are displayed.
TO CHANGE the order in which sequences are displayed
1. Select a sequence name by clicking on it.
2. Hold down the mouse button and drag the sequence to a new position.
NOTE: Altering the sequence order does not affect the order of sequences in the results windows, until you regenerate the results.
To view the new sequence order in the results windows, select the results button to display the Alignment Views dialog box. Then do one of the following:
- If you have a ClustalW alignment, select Recalculate and use the Alignment Views dialog box to repeat the ClustalW calculation
- If it is not a ClustalW alignment, just select OK in the Alignment Views dialog box to regenerate the windows.
SETTING REFERENCE sequences
In linear mode, you can keep reference sequences at the top of the list and compare them to others. Only the topmost of the scrollable sequences can be made into a reference sequence.
TO SET reference sequences
1. Ensure that the MSA display is in linear mode, by clicking the mode icon if necessary.
A pin icon will be visible to the right of the sequence name.
2. If necessary, click on the pin to "push it in."
The sequence is now stationary. It will remain at the top of the list while the other sequences are scrolled underneath. A new pin icon appears to the left of the sequence under the reference sequence.
NOTE: Further sequences can be locked as reference sequences whenever a pin icon appears. You may first need to change the sequence display order to place the required sequence below the existing reference sequences.
RENAMING ALIGNED sequences
After a sequence alignment, it is often useful to rename aligned sequences.
TO RENAME an aligned sequence
1. Select a sequence name by double-clicking on it.
The New Sequence Name dialog box is displayed.
2. Type a name in the New sequence name text box.
3. Select OK to save the renamed sequence.