Geneious Tips and Tricks

Split View

The split view button provides options for splitting the view so that multiple views are shown simultaneously for one document. For example, for a tree document, you could choose to view the tree and alignment simultaneously.

Circular Overview

For a plasmid or any circular sequence, you could choose the Circular Overview, set via General Tab. It presents a synchronised zoomed-out view of circular sequences alongside their linear view. Very helpful for staying orientated with synchronized editing, selection and scrolling.

Expanded View

The expand button expands the document view panel to fill the main window by hiding the sources panel on the right and the document table above. Clicking this again will return the layout to its original state.

Plugins

Plugins extend the features that are available in Geneious. You may navigate to the plugins interface by selecting the Tool tab at the top, and choosing Plugins. This will take you the “Plugins and Features” tab, which lets you manage downloadable plugins for Geneious. You will see a list of plugins which are currently available for download from the Geneious website which aren’t already installed. Each plugin is listed with a status which can be a star (for exciting plugins), New, or Beta. Click the Info button to read more about the plugin or click the Install button to download and install it. Once you’ve installed a plugin it will be listed within the Installed plugin window. Click the uninstall button next to a plugin to remove it.

Aliases

From Geneious R10 it is possible to store a single document in multiple folders simultaneously using Paste Alias in the Edit menu or by holding Ctrl+Shift when dragging (Cmd+Alt on Mac). This will create shortcuts to the original document, avoiding redundancy. Aliases will stay synchronised, so any change in the original document will be automatically applied to the aliases and vice versa. The alias source can be reached by right clicking on an alias document and selecting Go to Alias Source.

Multiple Folder Selection

Operations using sequences stored in different folders can be performed as following: simultaneously select the desired folders (by holding down ctrl or cmd on Mac) and perform the desired operation (i.e. Alignment of two sequences in two different folders). The result of the operation will appear in the folder selected in first place.

Sequence Selection

Selections on sequence documents can be performed by:

  • Clicking and dragging along the sequence
  • Clicking at the start point, holding the shift key and then clicking at the end point
  • Using the Go to Base tool, available under the Edit menu

Set Memory Allocated

For setting the memory allocated to Geneious, open Geneious → Preferences and go to the General tab. You should never allocate the total memory of your computer to Geneious, as you need to leave some RAM available for your operating system. As a general rule of thumb, on a 64-bit machine with up to 8GB of RAM in total you can allocate half the RAM to Geneious. On machines with more than 8GB RAM you should leave 3-4GB spare for your operating system and allocate the rest to Geneious.