franck,
I think you right to araise thise question, because it's not so clear for many of us, loof for example the presentation of MuSE :

MusE is a MIDI/Audio sequencer[...]
[...]
Jack they don't talk about qjackctl, it's the same for many software using midi as control or format.
It's interesting to discuss, it's true that we used qjackctl with alsa sequencer and it's true that the audio & midi in this apps are completly separate!
always interesting to look at the Dave Phillips page : http://linuxsound.atnet.at/ because there is plenty of tools to do it!!
thanks to light my view on this point :-)

I will test you stuff!

juto
Ahm, sorry, since when does Ardour do midi? ;)

No, I looked it up on the website of Jack now, and there's not a hint
of the word Midi there. I know, that there is an unpublished midi
suport for Jack in the works, which seems to have some legal problems
to be sorted out, but none of the official versions of Jack support
midi.

Maybe you are thinking about the midi connections tab in qjackctl??
This has nothing to do with Jack itself but it is a conneciton manager
for the ALSA sequencer. To use Pd with that, you need to load the
snd-virmidi module which creates ALSA sequencer enabled rawmidi
devices. Search google for me and the "Softsynth and Midi Howto".

Ciao