CoaSim: A Flexible Environment for Simulating Genetic Data under Coalescent Models

Mailund, Mikkel Heide Schierup, Christian Nørgaard Storm Pedersen, Peter Mechlenborg, Jesper N Madsen, Leif Schauser

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    Abstract

    Background Coalescent simulations are playing a large role in interpreting large scale intra- polymorphism surveys and for planning and evaluating association studies. Coalescent of data sets under different models can be compared to the actual data to test different evolutionary factors and thus get insight into these. Results We have created the CoaSim application as a flexible environment for Monte various types of genetic data under equilibrium and non-equilibrium coalescent variety of applications. Interaction with the tool is through the Guile version scripting language. Scheme scripts for many standard and advanced applications these can easily be modified by the user for a much wider range of applications. interface with less functionality and flexibility is also included. It is primarily exploratory and educational tool. Conclusions CoaSim is a powerful tool because of its flexibility and ease of use. This is illustrated varied uses of the application, e.g. evaluation of association mapping methods, bootstrapping, and design and choice of markers for specific questions.
    OriginalsprogEngelsk
    TidsskriftB M C Bioinformatics
    Vol/bind6
    Nummer252
    ISSN1471-2105
    StatusUdgivet - 2005

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