I believe Stockfish supports chess960. Stockfish is very strong and is free.
You will need a GUI to go with it, and there are dozens to choose from, many of which are also free.
Chess960 Computer Analysis
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Just finished my first 2 games of chess960, I would like to run computer analysis to see what I might have missed, but it doesn't seem to be available on chess.com. Can anyone recommend a good, engine for analysing games, preferable freeware or low priced that I can download or use online?