Troubleshooting PhyloWidget

All software has its flaws, and PhyloWidget is no exception.

Below is a checklist of potential issues and our recommended solutions; please let us know about anything not covered here!

  • General Problems

    • Browser crash / freeze-up
    • With certain versions of Firefox, Java, and Windows XP or Vista, we have observed the browser crashing entirely when PhyloWidget or any other Java applet is run. If this is happening to you, please visit and update your version of Java.

    • Sluggish / strange behavior

      The main point is this: Most strange or sluggish behavior in PhyloWidget can be fixed by restarting your browser!!

      Usually refreshing the browser will not fix problems with sluggishness. The Java runtime environment stays loaded for the entire time the browser is running, so the only way to give PhyloWidget a "fresh start" is to completely quit the browser, and then start it back up.

      To reiterate: If you're having a problem with PhyloWidget suddenly acting strange, 90% of the time restarting the browser will solve it!

    • OutOfMemory Error / Java heap space

      If you see either of these error message while using PhyloWidget, or the program appears to putter out when working with large trees or images, then the operation you attempted may be using more memory than is allocated to Java applets by default.

      The simplest solution is to download the standalone version of PhyloWidget from the homepage and run the program as an application, where more memory is allocated to the JVM.

      Another option is to edit your computer-specific applet settings to allocate more memory: see the relevant Java forum thread, or search Google for java applet heap space. One set of visual instructions for Windows XP can be found here.

    • Web links don't work

      On some browsers, especially Firefox, we have noticed PhyloWidget's "web link" popups getting blocked. If this is the case, configure your browser's popup blocker to allow to create popups.

    • Error pop-ups

      Some users, especially on Linux systems, have reported seeing pop-up messages mentioning Null Pointer Exceptions when trying to load PhyloWidget. If you see this, please submit a bug report!

  • Browser Compatibility Issues

    The fact that PhyloWidget is happy to live within a browser is convenient for quick, easy access online. However, browser support for Java is notoriously ill-formed, and despite our best efforts to maximize compatibility, some issues still remain. We can offer some very general advice:

    If you are on a Mac, we recommend using Safari to access PhyloWidget.

    If you are on a PC, we recommend using Firefox to access PhyloWidget.

    Here are some specific browser / OS issues that we have encountered:

    • OS X / Firefox 2.0: PhyloWidget's Toolbox components may be non-functional.

      Solution: use the Safari browser.

    • OS X / Safari: The screen flickers when the Node Info box is updated.

      Solution: Click "hide" to hide the toolbox and stop the updating.

    • Linux / Firefox: We have heard reports from users using the OpenJDK and/or IcedTea that PhyloWidget does not work with their system. If this is the case for you, please contact us so we can track down and fix the problem.

      Solution: use the Sun JVM on Linux.

  • Java Requirements

    PhyloWidget requires Java 1.5 or higher (this is also known as Java 5.0). Most modern systems, including OS X and Windows XP, should have this installed; if for some reason it appears that Java is not set up correctly on your system, simply visit to download the latest version.

Found a bug?

If you've found a specific, well-defined problem that doesn't fall under the categories above, then you probably found a bug in PhyloWidget. Sorry—it happens! If you have a few minutes to spare and are feeling particularly helpful, please do head over to our project site and submit a bug report.

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