• 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.  

  • 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 -classpath "$INSTALL_DIR$/jalview.jar:$INSTALL_DIR$/lib/*"
    jalview.bin.Jalview -open [FILE]

    Where $INSTALL_DIR$ is the InstallAnywhere installation directory.

    When compiling from source, use:
    java -classpath "$SOURCE_DIR$/dist/*"
    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

    Note: This FAQ has been updated - we no longer recommend the -Djava.ext.dirs=lib argument since it prevents Jalview from accessing some web services, and will be disabled in future versions of Java.

  • 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 !

  • On OSX Mojave, you may notice that sequences and IDs in the Jalview alignment window are hard to read. To fix this, first:

    1. Save your work and shut down Jalview

    2. Open a Terminal window (use spotlight or the Launcher and type 'Terminal' to locate the Terminal App), and type:


      defaults write -g CGFontRenderingFontSmoothingDisabled -bool NO

    3. Start Jalview again and load an alignment to check that the fonts are now legible.

    Thanks to Marcin for reporting this issue and testing the workaround via issues.jalview.org/browse/JAL-3134


  • When Jalview is run on WIndows machines with high resolution displays (e.g. 4K, retina, etc) resolution screens, you might find that all the menus, window titles, and alignment data are really tiny. That's because on high-resolution displays, all the windows and fonts have to be magnified so that you can read them, and the fix is to ask Windows to do the same for the Jalview application.

    Instructions on how to do this can be found in several places on the 'net. Your milage may vary so please let us know if you are having problems via the jalview-discuss AT jalview.org mailing list !

    See https://pivotce.com/2017/12/11/fix-java-applications-for-high-dpi-display/ for the following solution which should work for launching Jalview via webstart on machines with Java 8 installed.

    1. Close Jalview
    2. Find java.exe and/or javaw.exe
       (for pre 2.11.0 likely found in C:\Program Files\Java\jre(version#)\bin
        for 2.11.0 and later this can be found in %APPDATA%\Local\Jalview\jre\bin)
    3. Right click on it and select -> Properties
    4. Go to Compatibility tab
    5. Check Override high DPI scaling behavior.
    6. Choose System for Scaling performed by:
    7. Click OK
    8. Relaunch Jalview


  • If you've been redirected to this FAQ then it probably means that the Jalview Native application has encountered an error whilst trying to start. Here are some tips for various problems:

    Problems on Windows:

    If your installation of Jalview goes fine, but double clicking on the Jalview icon does not produce any error message, window or any other activity (other than the spinning blue circle) this might be caused by a space character in Jalview's installation folder.  To fix this:

    1. Uninstall the non-working Jalview by either:
      • Open the Control Panel and go to Programs→Programs and Features→Uninstall a program.  Select Jalview from the program list and then click on the Uninstall/Change button above the list.  This will launch Jalview's uninstall wizard, follow the instructions.
      • Open a File Explorer and go to location %APPDATA%\Local\Jalview\uninstall.exe or %LOCALAPPDATA%\Local\Jalview\uninstall.exe if the first one isn't found.  This should launch Jalview's uninstall wizard, follow the instructions.
    2. Install Jalview again using the same installer as before, but this time on the second screen (Select Destination Directory) ensure the path has no spaces (e.g. type in C:\Jalview)

    Problems on linux:

    1. If you have used the Jalview-X_unix_installer_x_x_x-j8.sh installer, or the similar *-j8.tar.gz distribution, in some cicumstances you might get an error when launching Jalview that includes the message "Failed to rename ./jre.tgz_new to ./jre.tgz":

    This (slightly misleading) error message is caused by the launcher not being able to find the right version of the Java runtime environment (JRE).

    For Jalview or later we distribute an installer for linux with 64bit intel processors that bundles a JRE, we recommend using this installer to upgrade.  For other linux platforms please read below.

    In the case of Jalview 2.11.0 this should be Java 1.8. You can fix this by installing the right version of Java either with your distribution's package manager. e.g.
    On Ubuntu 18.04,

    sudo apt install openjdk-8-jre

    On CentOS 8 or Fedora 31

    sudo yum install java-1.8.0-openjdk

    or you can install a local version of the Java runtime environment -- we recommend the installers from AdoptOpenJDK.

    If after installing a Java 1.8 runtime environment you are experiencing the same problem, you may need to tell the Jalview launcher where to find the JRE 1.8 with the environment variable INSTALL4J_JAVA_HOME_OVERRIDE. You can achieve this on the command line with, e.g. (assuming you installed Jalview in the default location ~/opt/Jalview)
    On Ubuntu 18.04,

    INSTALL4J_JAVA_HOME_OVERRIDE=/usr/lib/jvm/java-8-openjdk-amd64 ~/opt/Jalview/Jalview

    On CentOS 8 or Fedora 31

    INSTALL4J_JAVA_HOME_OVERRIDE=/usr/lib/jvm/jre-1.8.0 ~/opt/Jalview/Jalview

    Alternatively you could add an "export INSTALL4J_JAVA_HOME_OVERRIDE=..." in your ~/.bashrc file but this could affect other applications installed using install4j.

    Jalview will use a Java 11 runtime environment in version 2.12.

    2. If you have the openjdk-8-jre-headless package installed but NOT the openjdk-8-jre package (for example this might be default on an Ubuntu Server distribution) then you might find Jalview silently fails to launch and the ~/opt/Jalview/launcher.log file contains:

    Exception in thread "Getdown" java.awt.AWTError: Assistive Technology not found: org.GNOME.Accessibility.AtkWrapper

    To fix this you can either install openjdk-8-java with

    sudo apt install openjdk-8-java

    or comment out the following line "assistive_technologies=org.GNOME.Accessibility.AtkWrapper" in the file /etc/java-8-openjdk/accessibility.properties. You can do this with

    sudo sed -i -E 's/^(assistive_technologies=org\.GNOME\.Accessibility\.AtkWrapper)/#\1/' /etc/java-8-openjdk/accessibility.properties

    Other problems:

    Depending on your platform you will need to take a look at the launcher.log file within the Jalview installation directory:

    • On Windows the Jalview installation directory defaults to %APPDATA%\Local\Jalview,
    • On Linux/Unix the Jalview installation directory defaults to ~/opt/Jalview,
    • On macOS the launcher.log file can be found in /Applications/Jalview.app/Contents/Resources/app. To get here in Finder right click on the Jalview icon in Applications and select "Show Package Contents".  You can then click through to Contents → Resources → app . Warning!  Editing or deleting files in the Jalview.app package might result in your Jalview installation breaking!


  • If you are running Jalview in Linux with a HiDPI or 4K monitor then the font size and menus are likely to be too small to be practical.

    UPDATE: Jalview and above should automatically detect a Linux HiDPI display, and scale the application appropriately if you are using the Java 11 version. You can download a newer installer from https://www.jalview.org/getdown/release/install4j/11/jalview-2_11_1_1-linux_x64-java_11.sh (coming soon!).
    A previously installed version of the Java 11 version of Jalview should update automatically and will apply the HiDPI scaling the NEXT time it is launched after it auto-updates.
    Please note that we have found a "drag-and-drop" positional error in the underlying Java components when using upscaling in Linux.  This is detailed below.

    ORIGINAL: To effectively remedy this, you will need a Java 11 version of Jalview.  For Jalview Java 11 is not officially supported but we are working towards that, so you can:

    1. Download a Java 11 linux installer from https://www.jalview.org/getdown/release/install4j/11/jalview-2_11_1_0-linux_x64-java_11.sh
      (if you are using linux a platform other than intel 64 bit you will need to obtain a Java 11 JRE, e.g. from https://adoptopenjdk.net/, and then download the non-bundled-jre unix installer from https://www.jalview.org/getdown/release/install4j/11/jalview-2_11_1_0-unix-java_11.sh).
    2. Install as usual with the command
      bash jalview-2_11_1_0-linux_x64-java_11.sh
    3. Assuming this installed into the directory ~/opt/jalview, edit the file ~/opt/jalview/jalview and add onto the first blank line
      export GDK_SCALE=2
      so that the top of that file looks like
    export GDK_SCALE=2
    # Uncomment the following line to override the JVM search sequence
    # Uncomment the following line to add additional VM parameters

    Jalview should now run at double sized resolution.

    DRAG-AND-DROP ISSUE: When running Jalview (or any Java Swing application) with a scaling larger than 1 (most likely 2), the positional calculation when a drag-and-drop event occurs appears to be incorrect. This is most obvious when, for instance, dragging an alignment file from your file manager application onto Jalview when you have an existing alignment window open.  If you drop the file over the existing alignment, the new file should be appended to the existing alignment.  If you drop the file over Jalview but not over an existing alignment it should open in a new alignment window.  Because the drop event's position is miscalculated the results can be unexpected.  See the issue JAL-3702 for more details.

    For consistent behaviour, use the Jalview menu File→Input Alignment→From File to open a new alignment window.  To append to an existing alignment window use that alignment window's File→Add Sequences→From File option.

  • If you are running Jalview in Ubuntu Linux and think that fonts look incorrectly sized, like the following screenshot,


    you can turn off the Ubuntu system default (for Java swing applications) Gtk "Look and Feel" by running Jalview with the environment variable JAVA_TOOL_OPTIONS by running Jalview with the following command:
    JAVA_TOOL_OPTIONS="-Dswing.systemlaf=javax.swing.plaf.metal.MetalLookAndFeel" ~/opt/jalview/jalview


    To make this option always apply you can edit the file


    (or the script "jalview" in the directory you installed Jalview into) and add the following to the as the second or third line:

    export JAVA_TOOL_OPTIONS="-Dswing.systemlaf=javax.swing.plaf.metal.MetalLookAndFeel"

    so that the top of the script should look like:

    export JAVA_TOOL_OPTIONS="-Dswing.systemlaf=javax.swing.plaf.metal.MetalLookAndFeel"
    # Uncomment the following line to override the JVM search sequence
    # Uncomment the following line to add additional VM parameters


    Note that if you are also having problems with the Jalview interface appearing too small on a high resolution (HiDPI or 4K) monitor then also see the FAQ Jalview's Menus and Fonts are too small on my Linux machine


    Jalview uses a launcher (called getdown, see https://github.com/threerings/getdown) that runs an auto-updater for Jalview and verifies Jalview files by checking the Jalview web site.  Whilst the launcher checks for existing system proxy settings, sometimes it does not find those settings.  In this case it may pop up a window asking for proxy settings.  If this does not happen, and proxy settings are required, you can create a file called


    that should contain your proxy host and port like this:


    You should put the file in the same folder as the file getdown.txt:

    •   In Windows this is the folder you installed Jalview into (by default this is %APPDATA%\Local\Jalview\)
    •   In macOS this is buried in the Jalview application bundle as Contents/Resources/app (by default /Applications/Jalview.app/Contents/Resources/app/)
    •   In Linux this is also the folder you installed Jalview into (by default this is ~/opt/jalview/).

    The current release ( does not pass settings from this file on to the Jalview application.  This will be fixed in a future release.  In the meantime you can configure the proxy for Jalview in Jalview's own Preferences (see Tools->Preferences->Connections).

  • If you have a problem launching Jalview that results in an error message on the splash screen reading

    "We were unable to download the necessary files after five attempts. You can try running the application again, but if it fails you may need to uninstall and reinstall."

    (like this screenshot:


    Then you should close the splash screen window and try and launch the Jalview application again.

    If this does not work, you should install the latest Jalview release (found at https://www.jalview.org/getdown/release/).  The latest installer can be installed on top of the old version.

  • Whilst the current release versions (2.11.1.*) of the Jalview installers run with a bundled Java 1.8 runtime environment, Jalview development is using Java 11 (a much more recent LTS version of Java), but is maintaining support for Java 1.8 especially for the current release versions.

    This means that Jalview can run using Java 11 (and in the not-too-distant future will probably drop support for Java 1.8).  There are some necessary small but significant differences in the way that Jalview is packaged for Java 1.8 and Java 11 which means it is not easy to run a Java 1.8 version using Java 11, but there are (at least) three easy ways in which you can obtain a version of Jalview to run in Java 11:

    1. Jalview Develop application: This is the development version of Jalview packaged as an application installer separate from the release version of Jalview.  It uses a recent build of the "develop" branch of Jalview, which will include features and functionality that have not yet made it into the more stable release version.  It will also auto-update like the release version when we deem the develop branch to be stable enough and want to add in some newer features.  Whilst Jalview Develop should be relatively stable (it's not a nightly release) the newer features might not have been extensively tested (e.g. on all operating systems) as they would be before going into the usual release version.  If you do find any problems then we encourage you to report this to us.
      Note that the Jalview Develop application comes with a Java 11 runtime bundled in the application so no other software is required.
      Jalview Develop is described at https://www.jalview.org/development/development-builds/ and downloadable from https://www.jalview.org/getdown/install4j/develop/.
    2. An unsupported Java 11 installer of the current release version of Jalview can be downloaded from https://www.jalview.org/getdown/release/install4j/11/.
      Like Jalview Develop this is an installer with a Java 11 runtime bundled with the application.  It will however clash with the supported Java 1.8 release version of Jalview if you have that installed as well.
    3. Jalview executable jar file: This is an all-in-one jar file that can be run very simply.  As there is no installer it does not create the file associations, or automatically update itself, like the Jalview release or develop versions.  It also has no bundled Java 11 runtime so you will need to install this separately either through your OS package manager, or via a third party Java 11 installation.  We recommend (and use) the Java runtimes from AdoptOpenJDK.
      You can download the Java 11 release version of the Jalview executable jar from https://www.jalview.org/getdown/release/jalview-all- (in general, look for the executable jar link on the download page, and change the "j8" in the URL to "j11").
      To run the executable jar you just need to run:
      java -jar jalview-all-VERSION-j11.jar
      with your Java 11 runtime java.  You might even be able to launch it by double-clicking on the jar file in a file manager!