User preferences can be changed by going to Tools → Preferences. This window can also be opened using the shortcut keys Ctrl+Shift+P (Windows/Linux) or command+Shift+P (Mac OS X). In the user preferences you can change data storage, memory and connection settings, install plugins, customize the appearance and behaviour, deﬁne shortcut keys, and set up sequencing proﬁles. Many of these options are explained in more detail in the next sections.
The tabs in the Preferences window are as follows:
This tab contains general setup options:
Install plugins and customize features in this tab, see section 1.2.6 . This tab can also be accessed via Tools → Plugins.
In the Appearance panel you can change the way the main toolbar and the document table look, and also show or hide the memory usage bar.
In the Behavior panel you can change the way newly created documents are handled, such as where they should be saved to and whether they are selected straight away. You can choose whether to store document history, and create active parent/descendant links (see section 6 )
Reset questions allows you to reset the questions where you have previously told Geneious to remember your preference. If you have checked “remember my preference” in a dialog window, that window will no longer appear. You can click the Reset questions button to get these windows to appear again.
In the Viewer panel you can set whether the same view settings are saved across documents of the same type.
This section contains a list of Geneious Prime functions and allows you to deﬁne keyboard shortcuts for them. Shortcuts that are already deﬁned are highlighted in blue. Setting shortcuts can help you quickly navigate without using the mouse and also allows you to redeﬁne shortcuts to ones you may be familiar with from other programs.
Double click on a function to bring up a window to enter your new keyboard shortcut. If you use one that is already assigned, Geneious will tell you what function currently has that shortcut.
Keyboard shortcuts can also be added from individual operation dialogs. When the setup options for a particular operation are opened, click the settings cog in the bottom left of the window and choose Edit keyboard shortcut to assign or edit a shortcut key for that function.
Here you can set the URL for the NCBI BLAST database, enter your NCBI API key if you have one, and specify which ﬁeld of the Genbank document should be copied to the “Name” ﬁeld in the Geneious document.
This tab has options for the management of trace ﬁles and assemblies, allowing you to set thresholds that assign sequences as low, medium or high quality. To change the default parameters or set up a new binning proﬁle, click the Default proﬁle then click Edit/View. The following options are available:
To create a new proﬁle, change the parameters how you wish then enter a new Proﬁle name and click OK.
Other options for managing quality bins are: