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Paper   IPM / Biological / 13197
School of Biological Sciences
  Title:   Construction Of Random Perfect Phylogeny Matrix
1.  M. Sadeghi.
2.  H. Pezeshk.
3.  C. Eslahchi.
4.  S. Ahmadian.
5.  S. Mah Abadi.
  Status:   Published
  Journal: Advances and Applications in Bioinformatics and Chemistry
  Vol.:  3
  Year:  2010
  Pages:   89-96
  Supported by:  IPM
Interest in developing methods appropriate for mapping increasing amounts of genome-wide 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 graph-theory 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.
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 Ω (nm).
We have developed software, RAPPER, based on this algorithm, which is available at http://bioinf.cs.ipm.ir/softwares/RAPPER

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