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

Thomas Mailund¹^,2 , Mikkel H Schierup¹ , Christian NS Pedersen¹^,3 , Peter JM Mechlenborg³ , Jesper N Madsen² and Leif Schauser¹^,2

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

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

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

author email corresponding author email

BMC Bioinformatics 2005, 6:252doi: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