• You need a computer that can run at least Java 1.7 to use the full Jalview application (unfortunately this excludes users with older Macs - sorry). If java is installed, then the 'Launch Jalview Desktop' link at the top should work (if your browser asks you to save the application-x-jnlp file or choose an application to run it with, look for 'Java Web Start', or locate your java installation directory and look for the javaws binary). You can also go to the Install Anywhere Web Installer download area area to get an installer for your platform.
    If you have Java 1.8 or later on in your browser (Firefox still provides this), you can try the web based version of Jalview - JalviewLite - right now by going to the applets page. The web based version doesn't let you print or access web services, but includes most of Jalview's core functionality.

    Linux users: To launch jalview via webstart on openJDK from your browser, you will need to install icedtea-netx, which provides the javaws binary.

  • Use the Mouse

     

     

     

    Use the cursor keys

     

     

    Edit Selected Region Only

     

     

     

     

    Press F2 to enter Keyboard Mode

  • Right-click on the 'Consensus' label for the consensus annotation track, and select "Copy consensus sequence".

  • 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. 

  • Yes, a quick reference PDF for an early release of Jalview 2 is here, but we haven't updated it for a while.

  • 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.  

  • Because of security restrictions, an applet may not read or write files on the local system. This is to protect you from a malicious applet storing a virus on your computer or deleting all your files. Only the Jalview Desktop can create, print or save images, alignment files and Jalview projects on your computer.

    You can usually send data you have opened in the JalviewLite applet to the Jalview Desktop using the "File -> View In Full Application" menu entry. This will only work if you can launch the java webstart version of the Jalview Dekstop, and in the current version, will not send any additional edits or other changes to the alignment data that you may have made after opening it in JalviewLite.

  • 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.txt in 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.

    When compiling from source, use:
    java -Djava.ext.dirs=$SOURCE_DIR$/dist -cp $SOURCE_DIR$/dist/jalview.jar
    jalview.bin.Jalview -open [FILE]

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

  • Jalview now exports images and graphics using the same settings as the alignment display window. Just set the font and font size, and the layout style (normal or wrapped) using the View menu.
    If you do want to specify portrait or landscape, you could use the File→Print dialog box, and redirect the output to a file.

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

  • One of the commonest causes of 'strange behaviour' that our users have reported seems to be Jalview running out of memory. Memory errors can cause some operations to fail silently - with no warning, annotations may disappear from the alignment window, and web service calculations (apparently) never finish.

    You should be able to see something in the error log - see the instructions for bug reporting on how to view this. If you do see 'Out of memory' or 'Cannot allocate stack' or 'HeapAllocationError' type messages, then you might be able to fix it by increasing the memory available to jalview.

  • 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.

  • Yes! Just remember to include the '-nodisplay' flag on the command line (and if in doubt, also include java -Djava.awt.headless=true to tell Java not to attempt to use the graphics environment)

    For example:

    java -Djava.awt.headless=true .. jalview.bin.Jalview -nodisplay -open ...
    

    The latest version of Jalview should run fine on a server without a graphics environment, but some operations may fail. If you encounter problems, submit a bug report.

  • This seems to be a bug that occurs if current JDK versions are installed. You can work around this bug by moving to the directory C:\IA_Installers\Jalview and specifying the JVM location from the command line eg:

    install.exe LAX_VM <path to java executable>

  • 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!

  • Some latest versions of Linux fail to install with InstallAnywhere and will generate error messages such as "error while loading shared libraries: libm.so.6: cannot open". The problem can be fixed by modifying the install.bin script, and also the Jalview script.

    cp install.bin install.bak
    cat install.bak | sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > install.bin
    sh install.bin

    cp Jalview Jalview.bak
    cat Jalview.bak | sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Jalview
    sh Jalview

  • 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"

  • This error (and others like it) is raised when an old version of the Jalview Webstart JNLP is being used to launch the latest version of the application (for instance, because you have created your own JNLP file in order to increase the memory available to Jalview).
    To fix, first make sure that you are using the latest version of the Jalview JNLP file (right-click or apple-click to save this link to a file) to launch jalview.

    If you are using the latest version of the JNLP then you need to open the Java Web Start console panel, and flush any application caches and remove any old versions of Jalview listed in the application viewer. To do this:

    1. Locate and open the java console on your system (in your control panel or systems settings, but may also be in the Utilities section of the Applications folder on OSX.
      If you have access to a terminal, you can usually open the console with
      javaws -viewer
    2. Locate any jalview instances in your applications cache and remove them (usually, select the application and hit the delete or 'X' button)

    Once you've cleared the cache, try to run the Jalview JNLP file again.

  • The OSX InstallAnywhere version of Jalview is downloaded as a ZIP archive (install.zip) which is normally unpacked automatically to create an application called 'install' that you can run. If nothing happens when you double click the application, then there are a few things that could go wrong.

    Installer doesn't launch because it was unpacked with a third-party archive tool

    If you have chosen an alternative archive program for OSX to use to unpack ZIP files, then it probably didn't set the executable permissions for the application after it unpacked it. The easiest solution is to right or option click the install.zip that you downloaded, and choose 'Open with -> Archive Utility (10.X)' (where X is the numeric version of OSX that you are running); this will create a new 'install' application (probably called 'install 2') that you can now launch.

    If using a different archiver doesn't work, or you are working from the console, then you need to delve into the installer's application directory. Open the console, cd to the directory where the install application is located (probably ~/Downloads), and type:

      chmod u+x install.app/Contents/MacOS/install
      open install.app
    

    Permissions problems result in an error shown in the OSX Console window that reads something like

    ([0x0-0x6a86a8].install[25620]) posix_spawn("/Users/jimp/install.app/Contents/MacOS/install", ...): Permission denied

    If you see anything else, paste it into the search box on http://issues.jalview.org to see if it has been reported.

    Related bugs in the Jalview Issue Database: JAL-746.

  • Here are some symptoms we've observed when Jalview has failed to launch via webstart, or the Jalview installAnywhere could not be run.

    In all cases, the Web start file (jnlp) and the Installer downloaded and unpacked successfully.

    • Running the installer/jnlp file opens a "This program cannot be run because it comes from an unidentified developer".
      • For some reason, your Mac has not recognised our Apple Developer Signature (if you are running Jalview 2.8.1, please tell us about this!)
      • Follow step 1, below - select the 'Run anyway option'
    • Running the installer opens a "This file is damaged and should be moved to the trash"
      • In this case, your Mac thinks someone has tampered with the installation program, although actually, what has happened is that you've probably just downloaded a new version of Jalview. 
      • You need to follow step 2 below - temporarily disable the security check
    • Installer downloads but double clicking it does nothing.
      • This usually means that there is something wrong with your Java installation.
      1. Control-click the install-jalview  package and select the "Open Package Contents" option.
      2. Double click through the directories: ContentsMacOS
      3. Double click on 'install-jalview' (or 'install', for older Jalviews) - this will open up a terminal window with some commands that execute the installer program.

    Changing the gatekeeper settings

    First, open your system settings panel, and go to the security and privacy section:

    Step 1. If you see a prompt like the one saying ‘Open anyway’, then click it to launch the program.


    Step 2. If you don't see a prompt like the one above, then:

    • You'll need to click the padlock so you can make changes to the security settings, and then select the 'Anywhere' button.
    • Then try launching the installer or the application again.
    • Once you've launched the program you can return to the gatekeeper settings and switch back to your original security settings.
  • For some reason, your DAS registry setting might have become corrupted. Here's how to fix it:

    1. Launch the Jalview desktop (IMPORTANT: if you have more than one instance running already, close all but one).
    2. Go to the Tools->Preferences option to open the preferences panel.
    3. Open the 'DAS Settings' pane in the preferences panel - if you can't see it, click on the right most tab ('Editing' in my screen), and then the '>' icon to scroll to the next tab along.
    4. Replace the existing URL in the 'Use registry' text box with: "http://www.dasregistry.org "
    5. Click 'Refresh Available Sources' - you should see lots of sources appear in the list
    6. Hit OK in the preferences dialog box. This saves your preferences.
    7. Shut down Jalview, and then start it again and open the 'Fetch Sequences' dialog box to check that you can see all the sequence databases.
  • 1. In System Preferences, launch Java which opens Java Control Panel.
    2. On the "General" pane, click "View..." which opens Java Cache Viewer
    3. Select Jalview
    4. Click icon for creating a shortcut.  A Mac alias is installed on your Desktop.  Drag it to /Applications or wherever you want it.
    5. Double-click the Jalview alias file to launch.

    The first time it will download all of the jalview objects into cache again. Subsequent launches will only check for any updates, then launch.
    Note: This assumes you have Oracle Java 1.7 installed and have already run and downloaded jalview.
    [Authored by Dr Mark Saper, June 2014]

  • One of the Jalview team just got a Surface Pro 3 tablet and so naturally wanted to install Jalview on it. This is pretty straightforward, but some of the steps are slightly confusing if you aren't too familiar with running Jalview.

    1. If you do the Java webstart option the machine says it does not know what to do with the .jnlp file, so sends you to the App store to find an app that can open it. Unfortunately, the "app" it needs (Java) is not in the App store, so you get nowhere.

    2. What you have to do is go to www.java.com and install Java first from there.

      This should go fairly smoothly (it did for us - tell us if you have problems!).

    3. Once you have Java installed, Shut down your browser, then open it again and click on the Jalview webstart option again from the Jalview home page.

      If you don't restart your browser, Jalview won't start automatically and you'll need to locate the jalview.jnlp file and open it with the Java webstart application manually.

    Jalview and Multi-Touch
    Jalview is not yet muti-touch-aware, so drag, pinch to zoom etc don't work. Cascading menus also always cascade to the right regardless of the settings you make on the tablet for right or left-handed use, so you need to select menus with your left hand, or use the stylus left-handed.
    We'll be working on adding multi-touch in the future !

  • Jalview is compatible with Java 9, but only via webstart, or with a modified command-line launch script. If you use the InstallAnywhere version of Jalview it will recommend you install Java 8.

    If you have installed Jalview via InstallAnywhere and you cannot access JABAWS services (a dialog box appears after you start Jalview about this), then you can patch the Jalview installation.

    On OSX: - Add two lines to the Jalview.app/Contents/Info.plist file after the line starting <string>-Xdock:icon=

                                    <string>--add-modules=java.se.ee</string>
                                    <string>--illegal-access=warn</string>
    

    On Windows: Open the Jalview.lax file in Notepad (or another editor) # and locate and replace the existing lax.nl.java.option.additional line with

    lax.nl.java.option.additional=--add-modules=java.se.ee --illegal-access=warn
    

    Launching Jalview from the command line on Java 9

    To run Jalview 2.10.3 on Java 9, you need to add two additional JVM command line arguments:

     --add-modules=java.se.ee --illegal-access=warn

    Java 9 also ignores the 'java.ext.dirs' property so instead we recommend launching jalview via a script like:

    # set install path of jalview
    JALVIEWDIR=$DIR;  # change $DIR to where you built Jalview
    # compile the classpath
    CLASSPATH=`echo $JALVIEWDIR/*.jar | sed -e 's/r /r:/g'`
    # launch Jalview
    # you might also want --Xmx<memory in GB>G 
    java -classpath $CLASSPATH --add-modules=java.se.ee --illegal-access=warn jalview.bin.Jalview ${@};