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  1. Construction of random perfect phylogeny matrix
Construction of random perfect phylogeny matrix
635 viewed

Construction of random perfect phylogeny matrix

Sadeghi, M

Construction of random perfect phylogeny matrix

Sadeghi, M ; Sharif University of Technology | 2010

635 Viewed
  1. Type of Document: Article
  2. Publisher: 2010
  3. Abstract:
  4. Purpose: 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. Results: We introduce an O(max(n 2, nm)) algorithm for the random construction of such a phy-logeny matrix. The running time of any algorithm for solving this problem would be ω (nm). Conclusion: We have developed software, RAPPER, based on this algorithm, which is available at http://bioinf.cs.ipm.ir/softwares/RAPPER
  5. Keywords:
  6. Minimum allele frequency (MAF) ; Perfect phylogeny ; Recursive algorithm ; Tree
  7. Source: Advances and Applications in Bioinformatics and Chemistry ; Volume 3, Issue 1 , 2010 , Pages 89-96 ; 11786949 (ISSN)
  8. URL: https://www.dovepress.com/construction-of-random-perfect-phylogeny-matrix-peer-reviewed-article-AABC