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A method is described that uses the ABI PRISMTM 310 genetic analyzer in conjunction with custom-designed software to identify and classify RAPD products. This methodology will also work well with AFLPs and microsatellite analyses. The methodology uses the ABI PRISM 310's high-throughput (>500 samples per week) capabilities and in-lane molecular weight standards to efficiently separate and size DNA products. Peak detection, locus classification and export of the data in a form accessible by several genetic analysis programs were accomplished through a custom-written software program (Peaks©). Various criteria used by the program to identify and classify loci are described, and their effect on population analyses is examined. Criteria providing an effective, robust determination of population structure are presented.

The article discusses the technical aspects of 454 sequencing that altered the invention of pyrosequencing into a mega-throughput technology. According to the authors, 454 sequencing is based on pyrophosphate sequencing technology, where the reactions are conducted in a PicoTiterPlate, a partially etched plate of fused fiber-optic bundles containing roughly 1.6 million, 75 picoliter reaction wells. The authors discuss modifications to standard pyrosequencing and corrective software algorithms.