Notice
Since the tuning is very low, Pete uses PRS baritone guitars so that he can put thicker strings so the strings won't be loose.
The effects Pete uses could be either a phase of flange pedal.
Okay, I've seen Chevelle live and seen some pictures where Joe (the bassist) uses a 5-string Bongo MusicMan bass. He also uses a 4-string Stingray by MusicMan. The 4-string is for the songs with tunings as low as 1 1/2 steps down, B F# B E. But for the new songs, the tuning is lower by half a step for a total of 2 whole steps down. The strings are loose with the tuning, so Joe uses a 5-string bass for the new songs. I'm not 100% on the tuning.
Also see The Clincher video where the guitar tuning is Drop D down 2 whole steps (Bb F Bb Eb G C) and Joe is using a 5-string bass.
Here's a link of pic of Joe with a 5-string Bongo MusicMan bass.
http://us.ent2.yimg.com/musicfinder.yahoo.com/images/yahoo/epic/chevelle/012905_chevelle_0075.jpg