A new paper, "Making whole genome multiple alignments usable for biologists," by Daniel Blankenberg, et al. has been published (early access) in Bioinformatics. The paper describes "a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface."
The methods are described on a Galaxy Page as well.