When launched as an Application, Jalview automatically tries to
maximise the amount of memory allocated to it, but sometimes it may
run out of memory. This is because of the way that Java runs on a
computer - what is actually run is a program called a virtual
machine (the JVM) which executes the java instructions. The JVM has
limits on the memory that can be allocated to the java program - and
you might need to increase them if you are working with particularly
large datasets.
If Jalview has not explicitly told you that
it has run out of memory, then a common sign is that a function that
normally works seems to have no effect when working with a larger
set of sequences (this might include open dialog boxes for saving
PNG files, or when interpreting the result of a web service
calculation).
Jalview Memory Usage Monitor: If you are concerned about memory, or think that things might be behaving strangely because of a shortage of memory, then you can check this by enabling the memory usage monitor. This is done by selecting the Tools→Show Memory Usage option. Once enabled, the memory usage monitor displays the currently available memory, the total memory, and the percentage free at the bottom left hand side of the Jalview Desktop window's background.
Increasing the memory available to Jalview
Since Jalview 2.11, the program automatically configures the JVM memory settings to set the maximum memory available to Jalview to be 90% of physical memory.