You can use Edit | Add Sequences from File to add one or more sequences to a multiple sequence alignment.
This command is enabled when an MSA window is selected and the alignment is unlocked. If necessary, click on the padlock button to display an open padlock.
TO ADD sequences from a file
1. Choose where you want the sequences to be inserted, and position the cursor somewhere in the sequence line immediately above this point.
2. Choose Edit | Add Sequences from File.
The Open File dialog box is displayed.
3. Select the sequence file(s) you want to open.
4. Select Open to open the sequence files.
The sequences are inserted at the cursor.
For more information, see Editing alignments.