How can I see how much memory Geneious is using?

The memory usage bar, located under the Sources panel at the bottom left of your screen, shows how much RAM Geneious has available and how much it is using.  This can be turned on in the Preferences → Appearance and Behavior tab.

Note that Geneious runs inside a Java Virtual Machine, which itself will use memory.  Looking at JVM usage under Task Manager on Windows, or Activity Monitor on a Mac thus won’t give an accurate measure of how much memory Geneious itself is using, as it is the total RAM allocated to the JVM that users will see from the various monitors.

Note that the Geneious memory usage bar doesn’t include the memory used by external plugins such as the PAUP and PHYML plugins, as these run outside of Geneious.  

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    Stephanie Connon

    If I allocate 4G out of 8G RAM my Windows 7 machine has to Geneious will running the PHYML plugin be slower or faster than if Geneious had only 1G of RAM allocated to it?

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    Hilary Miller

    The amount of RAM you have available for the PHYML plugin won't make a difference to how fast it runs.  The RAM will determine the size of the dataset PHYML can handle (and it actually doesn't generally use a lot of RAM), but the speed at which it runs is determined by the processor speed of your machine.  There isn't any way to speed it up other than to use a machine with a faster processor.  For large phylogenies you might want to look at some of our other maximum likelihood tree-building plugins (Geneious R7 only) like Fasttree, RAxML and GARLI as these are likely to be faster.