Exporting a multiple alignment in FASTA format

You can create a FASTA format file from the aligned molecules. To do this:

1 Go to the main MultiSeq window and select File $\rightarrow$ Write alignment in FASTA format.

2 A Save as... window will appear. Select where you want to save the FASTA file. You may also change the name of the file in th eSave as: dialog.

3 Click the Save button.

Figure 25: FASTA menu

You also have the option of writing the secondary structure data into the FASTA file.
To do this:

4 Select File $\rightarrow$ Write secondary structure data in FASTA file.

5 A Save as... window will appear. Select where you want to save the FASTA file. You may also change the name of the file in th eSave as: dialog.

6 Click the Save button.

FASTA is a common alignment file, which enables you to study multiple alignments in many other applications.