SNAP: workbench management tool for evolutionary population genetic analysis.
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.


BACKGROUND
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.


BACKGROUND
A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu.
Price
Eric W
EW
Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
Carbone
Ignazio
I
D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D005828:Genetics, Population; D008957:Models, Genetic; D015233:Models, Statistical; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D018511:Systems Integration