I thought I would start posting papers that have mention that they have used PeakTrace. Here is the first of these posts — Phylogenetic Relationships of Muehlenbeckia, Fallopia, and Reynoutria (Polygonaceae) Investigated with Chloroplast and Nuclear Sequence Data published in International Journal of Plant Sciences, Vol. 172, No. 8. (October 2011), pp. 1053-1066. The authors of this paper claimed they were able to get 300 extra bases out of their reads using PeakTrace.