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This is a short documentation for Jalview 2.4, applet version. The full documentation can be found on Jalview website.

Jalview can be used to view and edit your multiple alignment. It can also save it in different formats, including PDF, PS, EPS or in several text-formatted outputs. Java 1.4 is required (see below for more information).
On a Macintosh computer, replace CTRL key with COMMAND key for cut/paste/copy actions.

Differences with Jalview 1.18
PS, EPS, PDF generation The main difference in the file generation process could be summarized as: WYSIWYG (what you see is what you get). You can add/remove/change things, and what you actually see on the screen (with or without annotations, wrapped or not wrapped, with different font size, etc...) will be redirected to an output file, in the same way as to a printer.

Sequence manipulation By pressing F2 one enters (or quits) the cursor mode. This allows navigation and editing of the alignment by using the keyboard.
Cursor mode
where n and m can be any number

use cursor keys to navigate in the alignment
n + C: goes to column n
n + S: goes to sequence n
n + P: goes to position n in the current sequence
n,m + RETURN: goes to column n and sequence m
n + SPACE: inserts n gaps
n + DEL: deletes n gaps
Q defines the top left corner of the selection area
M defines the bottom right corner of the selection area

Using mouse use SHIFT + left mouse to add/remove gaps in a sequence
use CTRL + left mouse to add/remove gaps in all sequences of the current selection, i.e. inside the red square

Miscellaneous Although the applet should work under java 1.4, there may be bugs (or annoying features) depending on your Operating System. Upgrading to java 1.5 (or later) should solve many of these problems.
When in an output text box, if there is no popup menu offering a "select all/cut/copy/paste" solution (and if the keyboard shortcut for "select all" -CTRL + A- is not working), you can try a SHIFT + left click combination (i.e. with the cursor standing at the beginning of the selection, go to the end of the selection and SHIFT + left click).
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J.
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench.
Bioinformatics 2009; 25(9):1189-1191.