Avidemux was recommended in answer to question 83711. My question is not quite the same, though it also concerns conversion of video files taken by a "landscape" camera which need to be converted to portrait mode
I have rotated videos (usually .MOV format) in Windows XP, using Apple Quicktime Pro ("QTP"). If done correctly the file remains rotated for other Windows machines without the need to retain the original as a reference file, as well as on an iMac, but nevertheless,using Kubuntu 12.04.1,appear in the original unrotated form in Dragon Player ("DP"). DP claims to be no more than a "simple, no frills" player, so I suspect that the problem is that QTP rotates files in a way that is accessible only by QT.
Does Avidemux do better? I need an application, if there is one, which will rotate a moving image so that it stays rotated on any computer!