There are currently two packages available for reducing your HIRES data: the MAKEE software written by Tom Barlow and HIRES Redux from Jason X. Prochaska.
The MAKEE package has been modified from the original version to handle the new
data format of the HIRES upgraded CCD mosaic.
For instructions on how to install and use MAKEE, and detailed descriptions of the package and its output data products, visit the MAKEE page. Look at the first part of the '0.WhatsNew' file in the download package for what's new for the new mosaic.