Saving Alignments

  1. Select Window $\Rightarrow$ Close All in the desktop window to close all windows.

  2. Selecting File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL from the desktop menu, enter in the dialog box and click OK.

  3. Open the overview window by selecting View $\Rightarrow$ Overview Window in the alignment menu.

  4. Select File $\Rightarrow$ Save Project as.. from the desktop menu and save the file on the computer.

  5. Close all windows, and load the project via File $\Rightarrow$ Load Project in the desktop menu.

  6. Select File $\Rightarrow$ Save As from the alignment menu. Save the file in fasta format (top of the list) in a folder on the computer, enter file name, select file format and click Save.

  7. Open the fasta file via File $\Rightarrow$ Input Alignment $\Rightarrow$ From File in the desktop menu. Compare how many windows open in both methods.

For more information on this topic go to section 1.5 of the Jalview manual.
 This exercise can be viewed in the Saving sequence alignments and projects video.