From the manual:
Analysing games
There are two analysis windows where two different engines can be configured to analyse the current board position.
Engines must be configured before in the Preferences Dialog. A default engine (Stockfish) comes with this installation and will be configured as first engine, if no other entries exist.
What's missing in the manual:
After successful configuration of an engine, go to one of the analysis panes, select the engine in the combo and press "Analyze" Button.
That's it.
For further topics (automatically analyzing games with engine, playing out games against the engine) refer to the corresponding manual sections.
ChessX GUI.
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