Yeah, but there is a link between this two topics, after
having analysed the harmonics I would like to create a sequence
of notes about it and automatically get chords that fit into
it...
In general, this is not an "easy" task.
I'm currently working (research) on the audio chord estimation (ACE)
topic.
For a "standard" song (polyphonic, poly-intrument) the accuracy is
still far from perfect (~75% of accuracy on a given, limited,
test-set).
However, for a single instrument, you can achieve good results with
a simple template matching.
You can't work directly on the FFT, but from the FFT you have to
calculate a 12-dimensional mid-level descriptor (called Pitch Class
Profile).
Then you can train your chord templates using a specified instrument
(i.e. if you want to estimate piano chords, you have to train your
templates with your piano).