Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Software

CoaSim: A flexible environment for simulating genetic data under coalescent models

Thomas Mailund12*, Mikkel H Schierup1, Christian NS Pedersen13, Peter JM Mechlenborg3, Jesper N Madsen2 and Leif Schauser12

Author affiliations

1 Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, 8000 Århus C, Denmark

2 Bioinformatics ApS, Høegh Guldbergsgade 10, 8000 Århus C, Denmark

3 Department of Computer Science, University of Aarhus, Høegh Guldbergsgade 10, 8000 Århus C, Denmark

For all author emails, please log on.

Citation and License

BMC Bioinformatics 2005, 6:252  doi:10.1186/1471-2105-6-252

Published: 14 October 2005

Abstract

Background

Coalescent simulations are playing a large role in interpreting large scale intra-specific sequence or polymorphism surveys and for planning and evaluating association studies. Coalescent simulations of data sets under different models can be compared to the actual data to test the importance of different evolutionary factors and thus get insight into these.

Results

We have created the CoaSim application as a flexible environment for Monte Carlo simulation of various types of genetic data under equilibrium and non-equilibrium coalescent processes for a variety of applications. Interaction with the tool is through the Guile version of the Scheme scripting language. Scheme scripts for many standard and advanced applications are provided and these can easily be modified by the user for a much wider range of applications. A graphical user interface with less functionality and flexibility is also included. It is primarily intended as an exploratory and educational tool

Conclusion

CoaSim is a powerful tool because of its flexibility and ease of use. This is illustrated through very varied uses of the application, e.g. evaluation of association mapping methods, parametric bootstrapping, and design and choice of markers for specific questions