Altering Alignment Layout

  1. Select Format $\Rightarrow$ Wrap from the alignment menu. Experiment with the various options from the Format menu, for example, adjust the column numbering, sequence ID format etc.

  2. Select Format $\Rightarrow$ Font and change the font parameters in Change Font dialog box. Place mouse on the alignment, hold down the middle mouse button and drag the mouse across the alignment, observe the effect on the fonts. Select Format $\Rightarrow$ Font and size 10 and style plain to revert to the default settings.

  3. Toggle the wrapped layout on and off by selecting Format $\Rightarrow$ Wrap.

  4. Toggle the annotation rows on and off by selecting Annotations $\Rightarrow$ Show Annotations.

  5. Individual annotation rows can be hidden by right-click on the annotation name and select Hide This Row from the context menu. Selecting Show All Hidden Rows will reveal the hidden rows.

  6. Annotations can be reordered by clicking on the annotations name and dragging the row to the desired location. For example click on the Consensus row and drag it to the top.

  7. The height of each annotation can be changed by placing the mouse on the annotation, holding the left mouse button down and dragging the mouse up or down.

  8. The white space between the alignment and annotation rows can be changed by moving the mouse near the top left-hand corner of the annotation labels until the up/down arrow symbol appears, then click and drag this icon. Note, this does not work in wrapped mode.

For more information on this topic go to section 3.2 of the Jalview manual.
 This exercise can be viewed in the Customising the appearance of the Jalview alignment window video.