Frusciante uses a wah pedal throughout for that funky, aggressive riff. Mesa Boogie amp with wah always on.
Signal Chain
Cry Baby Wah→Mesa Boogie Mark IV→4x12 V30→Output
PedalCry Baby Wah
mix
10
AmpMesa Boogie Mark IV
bass
5
gain
6
mids
7
treble
6
presence
5
Cab / IR4x12 V30
micSM57
mic positioncenter cap
Notes
Keep the wah moving constantly — it is not a static filter, it is an active rhythm element.