When you first launch SeqNinja, the Templates panel and Toolkit panel appear on the right. The Visual view on the left initially displays the SeqNinja Template Gallery, a list of shortcuts to items in the Templates panel.

If you plan to use the Visual View, simply click on a shortcut to begin your project. If you will be using the Text view, instead click the Text tab at the bottom of the window to get started.

The components of the SeqNinja user interface include:

Component Description
Scripts Multiple SeqNinja scripts can be open at the same time. Each script is represented by a tab above the Script view. To make a script active, click its tab. To close a script, click the ‘x’ on its tab.
Menus SeqNinja has six menus: File, Edit, View, Run, Window and Help.
Script View Displays your choice of either a Visual view or Text view. Select the desired view by clicking one of the view tabs at the bottom left of the script. Both views contain the same information in different formats.
Console panel The Console panel displays the output of the script.
Toolbar The toolbar contains items that can be used in one or more views. The Visual view and Console panel also have their own sets of tools.
Two docking areas These initially contain two docked panels and four expand bars:

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