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Paper IPM / Biological / 13197  


Abstract:  
Purpose
Interest in developing methods appropriate for mapping increasing amounts of genomewide molecular data are increasing rapidly. There is also an increasing need for methods that are able to efficiently simulate such data.
Patients and methods
In this article, we provide a graphtheory approach to find the necessary and sufficient conditions for the existence of a phylogeny matrix with k nonidentical haplotypes, n single nucleotide polymorphisms (SNPs), and a population size of m for which the minimum allele frequency of each SNP is between two specific numbers a and b.
Results
We introduce an O(max(n2, nm)) algorithm for the random construction of such a phylogeny matrix. The running time of any algorithm for solving this problem would be Î© (nm).
Conclusion
We have developed software, RAPPER, based on this algorithm, which is available at http://bioinf.cs.ipm.ir/softwares/RAPPER
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