Bioinformatics Advance Access originally published online on September 7, 2004
Bioinformatics 2005 21(3):402-404; doi:10.1093/bioinformatics/bti003
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Bioinformatics vol. 21 issue 3 © Oxford University Press 2005; all rights reserved.
SNAP: workbench management tool for evolutionary population genetic analysis
1 Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University Raleigh, NC 27695, USA
2 Department of Computer Sciences, North Carolina State University Raleigh, NC 27695, USA
*To whom correspondence should be addressed.
Summary: The reconstruction of population processes from DNA sequence variation requires the coordinated implementation of several coalescent-based methods, each bound by specific assumptions and limitations. In practice, the application of these coalescent-based methods for parameter estimation is difficult because they make strict assumptions that must be verified a priori and their parameter-rich nature makes the estimation of all model parameters very complex and computationally intensive. A further complication is their distribution as console applications that require the user to navigate through console menus or specify complex command-line arguments. To facilitate the implementation of these coalescent-based tools we developed SNAP Workbench, a Java program that manages and coordinates a series of programs. The workbench enhances population parameter estimation by ensuring that the assumptions and program limitations of each method are met and by providing a step-by-step methodology for examining population processes that integrates both summary-statistic methods and coalescent-based population genetic models.
Availability: SNAP Workbench is freely available at http://snap.cifr.ncsu.edu. The workbench and tools can be downloaded for Mac, Windows and Unix operating systems. Each package includes installation instructions, program documentation and a sample dataset.
Contact: ignazio_carbone{at}ncsu.edu
Supplementary information: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu
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