When the Allman Brothers Band were not forthcoming with any new material, Haynes and Woody left to concentrate full-time on Gov't Mule in 1997.

They were joined by members of the Allman Brothers, the Black Crowes, Parliament/Funkadelic and the Derek Trucks Band for their 1998 New Year's Eve concert, released both in a two and four CD version as Live... With a Little Help from Our Friends.

The performances exposed some of the bands' influences, covering Neil Young, Free, Traffic, Jimi Hendrix, Little Feat, Humble Pie and Black Sabbath.

Haynes and Abts continued to do limited touring in the Fall of 2000 supporting Ben Harper and the Innocent Criminals as an homage to Woody.

Their subsequent "Smile at Half Mast Tour" that followed was named in reference to a poem Haynes wrote for Woody's funeral.

Bass contributions to the CDs came from Jack Bruce, formerly of Cream, John Entwistle of the Who, Mike Watt of Minutemen, Les Claypool of Primus, Flea of the Red Hot Chili Peppers, Chris Squire of Yes and Stefan Lessard of Dave Matthews Band among others.

Bassists included, among others, Dave Schools of Widespread Panic, Oteil Burbridge who already had filled Woody's former place in the Allman Brothers, Les Claypool of Primus, Victor Wooten of the Flecktones, George Porter Jr. of the Meters, Jason Newsted (formerly of Metallica), Greg Rzab formerly of the Black Crowes and the Buddy Guy Band, and Andy Hess, also formerly of the Black Crowes.

The 19th edition of the Jam took place on December 15, 2007[10] with performances by Grace Potter and the Nocturnals, Shelly Colvin, Jason Isbell, Jackson Browne, G. Love, Bruce Hornsby, Peter Frampton, and others.

The band titled their set "Old School Mule" and ran through some of their older songs such as "Wandering Child" and "Thorazine Shuffle".

On September 15, 2008, Haynes' wife, Stefani Scamardo [13] announced on her Sirius radio show[14] that Andy Hess would be leaving the band and a new bassist would be in place for the fall tour.

On August 17, 2009, it was announced on the band's official website that Gov't Mule's eighth studio album, By a Thread,[16] would be released on October 27, 2009.

[17] On the same date, the first track of the new album, "Broke Down on the Brazos", featuring Billy Gibbons of ZZ Top, was made available for listening on the website.

From the Gov't Mule web site: "Following in the tradition of 2007's Holy Haunted House and last year's Pink Floyd spectacular, the band, once again, has something very special planned for the occasion.

Previous sold-out shows had featured covers of Led Zeppelin's Houses of the Holy and an assortment of Pink Floyd compositions.

[21] On December 31, 2013, Gov't Mule performed with Robby Krieger, the guitarist from the Doors, at the Beacon Theatre in New York City.