There are two separate things that you can select in Overtone Analyzer: Individual Tones on the Piano Keyboard and the Overtone Sliders, and chunks of Audio Data that extend over a specific time range.
Selecting time range of a recording
Audio Data can be selected on the Timeline, the Waveform View, and on the Spectrogram. Simply click anywhere on these views, hold the left mouse button, and move the mouse to the end of the area that you want to select.

Modifying existing selection
You can click and drag the borders of an existing selection to make it larger or smaller.
Working with a selection
Once you have a selection, playback will play it in a loop. You can also apply the Zoom to fit selection command (either on the toolbar or through the right-click context menu) to expand or shrink the selection to fill the entire screen.
Further, you can apply edit commands such as Cut, Copy, and Crop to selection.
Locking a selection
If you click anywhere on the Timeline or in the Analyzer View, the playback cursor will jump to the position of the click, and the current selection will be reset.
Sometimes you might want to hold on to a selection a bit longer, but still move the cursor within the selection to hear specific parts. To prevent the selection from being lost when you move the cursor, click on Edit / Lock selection. Now the selection can still be resized by moving its borders, but clicking somewhere on the Timeline or Analyzer view won't destroy the existing selection.
Resetting the selection
If the selection is not locked, you can simply click on the Timeline or Analyzer view. This will reposition the playback cursor and reset the selection. You can also apply the Reset selection command through the Edit menu, the right-click context menu, or by pressing the ESC key.
Selecting Tones
You can select and deselect tones on the piano keyboard and on the Overtone Sliders by clicking on them while holding the Control key. To play those tones, click on Tools / Play selected tones.

To make all tones unselected click on Tools / Deselect all tones.