Linear amplification or cycle sequencing is an advance that has made the use of automated fluorescent DNA sequencing instruments truly practical for large-scale genome analysis. We have investigated several variations of our standard cycle sequencing method. First, we have reduced the number of amplification cycles, which resulted in improved data quality and faster sequencing. Second, we have used different thermostable enzymes, which again improved data quality. Lastly, we have devised a method for precipitating reaction products in 96-tube trays. Together, these variations have allowed us to develop an improved cycle sequencing method that significantly increases sequencing throughput, improves efficiency and data quality, and reduces the cost of sequencing reactions.