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Performs fragment analysis. Fragman is an R package that automatically scores DNA fragment lengths in diversity panels and biparental populations, and transforms the observed lengths into formats required for further genetic analysis in other software. The software can work with any DNA standard, can automatically and simultaneously analyze multiple samples and allows automatic scoring of diversity and biparental populations. It provides additional tools for analyzing and converting the data into other formats.

HiTRACE / High-Throughput Robust Analysis for Capillary Electrophoresis

Employs a series of automated techniques to control the high level of variability in parameters of capillary electrophoresis (CE) systems. HiTRACE resolves a key alignment bottleneck of modern nucleic acid structure mapping experiments. It consists of five major steps: (i) preprocessing, (ii) correlation optimized linear alignment, (iii) dynamic programming-based non-linear adjustments, (iv) sequence annotation and (v) peak fitting.


Allows quantitative analysis of nucleic acid reactivity information. ShapeFinder is an extension of the BaseFinder trace-processing platform and incorporates several tools based on signal-processing algorithm. The software permits users to: (1) convert measured fluorescence intensity to quantitative cDNA fragment amounts, (2) correct for signal decay over read lengths extending to 600 nts or more, (3) adjust reactivity data to the known RNA sequence, and (4) quantify per nucleotide reactivities using whole-channel Gaussian integration.