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QTractor supports Linux native VSTs, so there's the pizmidi collection of MIDI processing plugins:

http://www.kvraudio.com/forum/viewtopic.php?t=192282&start=0

Unfortunately those are realtime processors. What Nev and I want are things like these to be applied to a track(s) or any segment of a track in deferred time:

Track merge - Merge two or more tracks together
Note splits - Split notes from a track ccording to pitch, velocity, duration, modulus, etc.
Pitch randomization - Randomize according to specified key/mode (or not)
Track rebar
Transpose/Invert
Harmonic transposition/inversion
Retrograde - whole selection or only note-ons
Compex velocity/duration/etc.
Velocity scale/shift
MIDI CC map/scale/shift
Tempo transforms - accelerando/scale/shift/tap-tempo

It wouldn't hurt my feelings if these were all realtime operations as well. ;)

These transforms are only some of what I use in Sequencer Plus Gold. I'll be happy to list more, along with new ones I'd like to see. :)

Best,

dp