Is there a service like skyscanner for trains?
I mean a comprehensive web service including all train companies' timetables so I'm sure I'm not ignoring any train connection.
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Yes. Bahn.de (english page) offers timetables and a trip planner for European train travel.
The rail travel site Seat61 mentions a couple of quirks and suggestions regarding Bahn.de (under "How to check European train times"):