You can also use ffmpeg and the commandline (taken from Rotating videos with FFmpeg):

Rotate 90 clockwise:

ffmpeg -i in.mov -vf "transpose=1" out.mov

For the transpose parameter you can pass:

0 = 90CounterCLockwise and Vertical Flip (default) 
1 = 90Clockwise 
2 = 90CounterClockwise 
3 = 90Clockwise and Vertical Flip

And to flip it horizontally (ffmpeg documentation):

Flip the input video horizontally.

For example to horizontally flip the video in input with `ffmpeg':

ffmpeg -i in.avi -vf "hflip" out.avi

Nota bene 1

Older versions of Ubuntu supplied avconv instead of ffmpeg. In this case just change ffmpeg to avconv:

avconv -i in.mov -vf "transpose=1" out.mov

Nota bene 2

If the output is a .mp4 video you has to add strict -2 before the output file to avoid error message :

ffmpeg -i in.mp4 -vf "transpose=1" -strict -2 out.mp4