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If you finish a ride and your chainstay has no paint left, your tyres were too wide for the clearance offered. ;)
5mm sounds good. Mine were 2mm with 35s and that looked way too close if I was to ride anything slightly muddy. But if you're definitely riding muddy then 5mm is probably too close too.
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Is there a minimum recommended clearance between tyres and seat/chain stays?
Depends what surfaces you're riding on. If you're riding on mud, you need clearance for mud. If you're riding on silky smooth perfect roads, and your wheels are as stiff as hell, you don't need much clearance at all.
5mm is a reasonable starting point though. I'd be a bit wary of having much less, even on a road bike.
Is there a minimum recommended clearance between tyres and seat/chain stays?
Or a rule of thumb as with mudguards, which is 5mm.