Pulse field gel electrophoresis mapping is an important technique for characterizing large segments of DNA and constructing long-range restriction maps. We have developed a tool, PFGE MAPPER, to aid in the construction of pulse field electrophoresis gel maps. This tool helps construct pulse field gel maps from single and double digest experiments visualized by hybridization with single copy probes. The program is written in Think C and runs on Macintosh computers. An intuitive interface allows the user to interactively modify fragment sizes or errors, select fragments for analysis and recalculate the maps. Maps can be printed or saved for later viewing. After constructing and saving several maps in a region, PFGE MAPPER can be used to refine and extend the overall map by merging individual maps. This tool should be useful for constructing long-range restriction maps of genomic DNA and yeast artificial chromosomes.