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, post a message on the Jalview Discussion Forum describing the problem, and someone will take it from there.