Many genomic scale projects rely on the efficient and accurate identification of clones from an ordered library. The most direct way of identifying clones is through hybridization to high density filters. To increase the throughput many laboratories have explored the automation of this process, but they have been hampered by the lack of suitable software for the process. The Clemson University Genomics Institute is a major supplier of high density filters to laboratories throughout the world. The development of a software package to analyze these filters will be carried out to greatly facilitate their use. Researchers in laboratories which receive the filters will also receive the software package in order to allow the implementation of automated clone identification.