On this page you can request a whole-genome alignment between two genomes that are on the UCSC Genome Browser. Such alignments can take thousands of compute hours to produce. The alignment here will be generated on the Galaxy platform, using a workflow that uses the TACC high performance compute GPU resources. The full process may take up to a few days. You will receive an email when it is complete.
Once complete, you will find two new tracks on both assemblies, one with the full alignment results ("all chains"), and one track with the best alignment (single coverage) for every basepair, which can be used for "liftOver". Since these tracks are single-coverage on the current genome, the alignments are reciprocal so one is produced per assembly. For more information on how to download these chain files and use liftOver, see also: Converting coordinates. Once these tracks are available, you can also use our Quicklift feature to lift annotations on-the-fly, as you use the browser, see also: Quick Lift guide for more information.
If one of the two genomes is not on the UCSC browser yet, please request it first on our Assembly Request Page, then come back here when the assembly has been added to the browser.