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Bioinformatics Vol. 19 no. 2 2003
Pages 289-290
© 2003 Oxford University Press

Applications Note

Simulating haplotype blocks in the human genome

David Posada * and Carsten Wiuf

Variagenics Inc., 60 Hampshire St, Cambridge, MA 02139-1548, USA

Received on June 26, 2002 ; revised on August 7, 2002 ; accepted on August 10, 2002

Summary: A bioinformatic tool was written to simulate haplotypes and SNPs under a modified coalescent with recombination. The most important feature of this program is that it allows for the specification of non-homogeneous recombination rates, which results in the formation of the so-called ‘haplotype blocks’ of the human genome. The program also implements different mutation models and flexible demographic histories. The samples generated can be very useful to better understand the architecture of the human genome and to investigate its impact in association studies searching for disease genes.

Availability: The SNPsim package is available at http://www.evolgenics.com/software

Contact: dposada{at}evolgenics.com

* To whom correspondence should be addressed.


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