There are several ways to align a pair of sequences using JAligner:

Command line

java -jar jaligner.jar <s1> <s2> <matrix> <open> <extend>



java -jar jaligner.jar s1.fa s2.fa BLOSUM62 10.0 0.5

In order to load a user-defined scoring matrix from the file system, the path to the matrix file has to include at least one file separator (a file separator flags JAligner to load the scoring matrix from the file system instead of looking it up in jaligner.jar).


java -jar jaligner.jar s1.fa s2.fa ./matrix.txt 10.0 0.5

The layout of a user-defined scoring matrix file is expected to be the same as the layout of the standard scoring matrices:

Java Network Launch Protocol (JNLP)

In general, JNLP-based applications require Java Web Start (JWS) to be installed on the client machine, fortunately, JWS has been bundled within the core Standard Java Edition (J2SE) since J2SE 1.4.

So assuming JWS is already installed, JAligner can be launched by visiting the XML deployment descriptor jaligner.jnlp at (http://jaligner.sourceforge.net/jaligner.jnlp) through the web browser or command line with the executable javaws, which exists under the javaws directory under the installation (root) directory of the Java Runtime Environment (JRE).


javaws http://jaligner.sourceforge.net/jaligner.jnlp

In jaligner.jnlp, a full permission is requested because the application needs access to:

But since jaligner.jar is signed by a self-signed certificate, once the download of the JAR file is complete, JWS displays a message warning that the application is requesting a full permission and the signing certificate could not be verified, so to bypass that warning message and to start the application, it is required to click on the "Start" button in the warning message window.


The command line to start JAligner as a desktop GUI application is

java -jar jaligner.jar

In addition, there are downloadable installers (built using ej-technologies's install4j) for the following operating systems (Linux, UNIX, Mac OS X and Windows).

Programming Application Interface (API)

Class SmithWatermanGotoh has the public static method align, that can be called programmatically to align two sequences.



If you are using JAligner in a published work or product, please cite:

Ahmed Moustafa, JAligner: Open source Java implementation of Smith-Waterman, (http://jaligner.sourceforge.net) (the date accessed).



I deeply appreciate all people who have contributed with questions, comments or suggestions regarding JAligner, every single feedback has been helpful and I have learned from it. I would like to express my special thanks to: