Jalview Anatomy Jalview has two navigation and editing modes: normal mode (where editing and navigation are via the mouse) and the cursor mode (where editing and navigation are via the keyboard). Jalview always starts up in normal mode. The F2 key is used to switch between these two modes. With a Mac, the key combination Fn and F2 keys are needed (as the F2 key is often assigned to screen brightness).

  1.  Load an alignment from its URL, in the desktop window select File $\Rightarrow$ Input Alignment $\Rightarrow$ from URL. Copy the URL (https://www.jalview.org/examples/exampleFile_2_7.jvp) in the Input Alignment From URL dialog box and click OK. (The URL are stored in history, clicking the up/down arrow in the dialog box is an alternative way to access the URL.)

  2. Rearrange the windows on the desktop by placing the mouse in the title panel on the top of the window, then click-and-drag.

  3. Resize the windows by placing the mouse on the lower right-hand corner of the window, then click-and-drag.

  4. Scroll around the alignment using the alignment (vertical) and ruler (horizontal) scrollbars.

  5. Open the Overview Window, select View $\Rightarrow$ Overview Window in the alignment window. Reposition and resize the window.

  6. Click and drag the red box in the overview window across the alignment, and note the effect in the alignment window.

  7. Place the mouse cursor on a residue in the alignment window, view the status bar in the lower left-hand corner of the window. It contains information about the sequence and residue selected.

  8. Press the [F2] key, or [Fn]-[F2] on Mac, to enter cursor mode. The position of the cursor is indicated by a black background with white text. Use the direction keys (↑, ↓, ←, →) to move the cursor around the alignment.

  9. Move to sequence 7 by pressing 7 S. Move to column 18 by pressing 1 8 C. Move to residue 18 by pressing 1 8 P. Note that the residue and sequence number will be different positions if there are gaps inserted into the sequence.

  10. Move to sequence 5, column 13 by typing 1 3, 5 [RETURN].

  11. Press the [F2] key, or [Fn]-[F2] on Mac, to return to normal mode.

For more information on this topic go to section 1.3 of the Jalview manual.
 This exercise can be viewed in the Navigating the Jalview desktop video.