P eak S tudio: a tool for the visualization and analysis of fragment analysis files

Summary While emerging technologies such as next‐generation sequencing are increasingly important tools for the analysis of metagenomic communities, molecular fingerprinting techniques such as automated ribosomal intergenic spacer analysis ( ARISA ) and terminal restriction fragment length polymorphisms ( T‐RFLP ) remain in use due to their rapid speed and low cost. P eak S tudio is a java‐based graphical user interface ( GUI ) designed for the visualization and analysis of fragment analysis ( FSA ) files generated by the A pplied B iosystems capillary electrophoresis instrument. Specifically designed for ARISA and T‐ RFLP experiments, P eak S tudio provides the user the ability to freely adjust the parameters of a peak‐calling algorithm and immediately see the implications for downstream clustering by principal component analysis. P eak S tudio is fully open‐source and, unlike proprietary solutions, can be deployed on any computer running W indows, OS X or L inux. P eak S tudio allows data to be saved in multiple formats and can serve as a pre‐processing suite that prepares data for statistical analysis in programs such as SAS or R .