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We introduce a pipeline to easily generate collections of web accessible UCSCgenome browsers interrelated by an alignment. Using the alignment, allannotations and the alignment itself can be efficiently viewed with referenceto any genome in the collection, symmetrically. A new, intelligently scaledalignment display makes it simple to view all changes between the genomes atall levels of resolution, from substitutions to complex structuralrearrangements, including duplications.

Comparative Assembly Hubs: Web Accessible Browsers for Comparative Genomics