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Sadeghi M, Pezeshk H, Eslahchi C, et al. Construction of random perfect phylogeny matrix. Adv Appl Bioinform Chem. 2010;3:89-96doi: 10.2147/AABC.S13397.
Sadeghi, M., Pezeshk, H., Eslahchi, C., Ahmadian, S., & Abadi, S. M. (2010). Construction of random perfect phylogeny matrix. Advances and applications in bioinformatics and chemistry : AABC, 389-96. https://doi.org/10.2147/AABC.S13397
Sadeghi, Mehdi, et al. "Construction of random perfect phylogeny matrix." Advances and applications in bioinformatics and chemistry : AABC vol. 3 (2010): 89-96. doi: https://doi.org/10.2147/AABC.S13397
Sadeghi M, Pezeshk H, Eslahchi C, Ahmadian S, Abadi SM. Construction of random perfect phylogeny matrix. Adv Appl Bioinform Chem. 2010;3:89-96. doi: 10.2147/AABC.S13397. Epub 2010 Nov 16. PMID: 21918630; PMCID: PMC3170006.
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Adv Appl Bioinform Chem. 2010;3:89-96. doi: 10.2147/AABC.S13397. Epub 2010 Nov 16.

Construction of random perfect phylogeny matrix.

Advances and applications in bioinformatics and chemistry : AABC

Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi, Sara Ahmadian, Sepideh Mah Abadi

Affiliations

  1. National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

PMID: 21918630 PMCID: PMC3170006 DOI: 10.2147/AABC.S13397

Abstract

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 phylogeny 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.

Keywords: minimum allele frequency (MAF); perfect phylogeny; recursive algorithm; tree

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