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PubMed · 15353448

SNAP: workbench management tool for evolutionary population genetic analysis.

Eric W Price·Ignazio Carbone
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Abstract

UNLABELLED: 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. SUPPLEMENTARY INFORMATION: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu.

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Computer SimulationDNA Mutational AnalysisEvolution, MolecularGenetic VariationGenetics, PopulationModels, GeneticModels, StatisticalSequence AlignmentSequence Analysis, DNASoftwareSystems IntegrationJournal Article

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BibTeXRIS

Eric W Price, Ignazio Carbone. 2004-09-07. SNAP: workbench management tool for evolutionary population genetic analysis.. https://doi.org/10.1093/bioinformatics%2Fbti003

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