I usually download the zeranoe builds for ffmpeg, available at https://ffmpeg.zeranoe.com/
A simple example for encoding a HapQ movie and removing the audio from the file:
ffmpeg -i InputMovie.mov -an -vcodec hap -format hap_q HapQMovie.mov
-i specifies the input file, which can be just about any format
-an tells ffmpeg to remove any audio tracks
-vcodec (or -c:v) specifies which codec to use
-format specifies which hap flavour to use (hap, hap_alpha or hap_q)
The last argument is the name of the reencoded file.
For very large movies (high resolution, that is) it makes sense to use the -chunks n argument to enable multithreaded decoding, where n is the number of chunks to use. It never makes sense to use more chunks than there are cores in the target (display) computer. As each additional chunks adds a (very) slight overhead in the form of decreased decoding speed and larger files, it is generally a good idea to keep the number of chunks as low as possible.
For a list of codes supported by ffmpeg: ffmpeg -codecs
For help about a specific codec: ffmpeg -h encoder=x, where you would replace x by the name of the codec as listed by the ffmpeg -codecs command.