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Press F2 to enter Keyboard Mode

You may be using a keyboard which has visual / audio settings mapped onto the Function keys. You must press the "Fn" key, together with F2 key to toggle Cursor Mode. 

Versions of Jalview released before November 2012 did not include any special support for scoring or visualizing nucleotide sequences, although they could read, write and manipulate DNA and RNA sequences, and calculate a consensus.

Version 2.8 of Jalview was the first release to include special support for nucleic acid sequences, and included a substitution matrix that copes with both RNA and DNA symbols which can be used to calculate trees and principal component analysis plots from alignments. Nucleotide base pair patterns provided as WUSS or VIENNA dot-bracket annotation can also be visualised, and used to calculate base-pair consensus score and sequence logos. Version 2.8 of the Jalview Desktop also included VARNA for interactive exploration of 2D RNA structure. For the latest information about nucleic acid support, see the nucleic acid section of Jalview's help pages.  

Yes. The Jalview Desktop has a number of command line options, but how you access them depends on the way you want to launch Jalview:

1. If you use Java Web Start to launch Jalview, then on some versions of Java Webstart you can start up Jalview with a specific file by typing:

javaws http://www.jalview.org/webstart/jalview.jnlp -open yourFileName

This is fine for launching the desktop with prepared data, but less useful for batch processing since any console output will be written to the java console.

2. If you installed the InstallAnywhere version of Jalview you can run the application binary with additional arguments. However any output from the application will be sent to a file called output.txtin the directory where you installed Jalview, rather than to the command's standard output channel.

3. To use Jalview like a command line program from a terminal, we recommend you use the following command (you could also put this in a shell or batch script).

java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE]

(where $INSTALL_DIR$ is the InstallAnywhere installation directory or the dist directory created when building Jalview from source) 

Use -help to list the current set of arguments Jalview supports. The online documentation also includes a list of jalview command line parameters

Full instructions for different operating systems and installations are here. If yours isn't listed, drop us a line at the help address.

Firstly, see if you can reproduce the bug. Check Jalview's memory settings (Desktop->Tools->Show Memory usage) to make sure you have at least 50% memory free when testing this. If not, the problem might be because you ran out of memory when using Jalview.

Then, follow the instructions below to gather essential information regarding the bug:

• The Jalview desktop includes a Java Console - this is disabled by default, but if you enable it from the Desktop->Tools->Show Java Console menu item, a window will open that will contain the version of jalview and information about your operating system. 
• The jalview java console can slow down some operations. If it takes too long to reproduce your bug with the console open, then close it and try another way below:
• If you installed Jalview using Java Webstart, locate and start the program "javaws" or "javaws.exe" on your system. Then click the "Edit" menu, select "Preferences" then click the "Advanced" tab. Make sure you check the "Java Console" option to "Show Console", then click "OK" and restart Jalview. A Java console will be shown when Jalview starts up, and information about any problems should be output to the console window.
• If you installed Jalview with InstallAnywhere, you will find a text file in the directory in which you installed Jalview called "output.txt" Include this file with any bug report you have.

Prepare the input data and a description of how the bug is reproduced

Prepare a copy of the alignment file you are using when you find the bug, and try to describe as fully as possible the steps you took before the bug occurred. If you can reproduce the bug with a simpler data set, then send us that instead!

Make a bug report !

If you are familiar with bug tracking systems, then you can register and submit a bug report directly to the Jalview Bug Tracker, otherwise, just send an email to the discussion mailing list describing the problem, and someone will take it from there.

We have tried to ensure that all files created in earlier versions of Jalview can be read in by later versions. If you have a Jalview format file which no longer loads, please let us know by emailing the file to us. It is possible other people are having the same problem!

In the application, open the preferences dialog window (Tools -> Preferences) Open the tab labelled "Output" and then select which file formats to which you do not wish to append "/start-end"

We publish Jalview using our own X.509 certificates. When launching Jalview for the first time, you will be asked if you would like to accept the signing certificate. Certificates are usually signed by the Barton Group (this information is in the technical details panel), and also include an expiry date. If you use a version of Jalview with an expired certificate you will get a 'Signer's certificate has expired' warning, but if you press 'OK' or 'Accept', you should still be able to launch Jalview.