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Does anyone know if an application exists where you can import multiple PGN files and layer them on top of one another?

It would be interesting to upload say 1,000 games and somehow visualise the most common moves for winning.

I was wondering if something like this exists?

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If I understood well what you are asking, you are looking for a chess database application. Yes, they exist, and there many examples. Among non-commercial ones you can find Scid and among commercial ones you have for example ChessBase.

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Chessbase can display piece probabilities for sets of games.

http://help.chessbase.com/Reader/12/Eng/index.html?000144.htm

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