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|Title:||Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns|
|Citation:||Journal of Computational Biology, 2008; 15(9):1133-1153|
|Publisher:||Mary Ann Liebert Inc Publ|
|Laxmi Parida, Marta Mele, Francesc Calafell, Jaume Bertranpetit and The Genographic Consortium|
|Abstract:||Traditionally nonrecombinant genome, i.e., mtDNA or Y chromosome, has been used for phylogeography, notably for ease of analysis. The topology of the phylogeny structure in this case is an acyclic graph, which is often a tree, is easy to comprehend and is somewhat easy to infer. However, recombination is an undeniable genetic fact for most part of the genome. Driven by the need for a more complete analysis, we address the problem of estimating the ancestral recombination graph (ARG) from a collection of extant sequences. We exploit the coherence that is observed in the human haplotypes as patterns and present a network model of patterns to reconstruct the ARG. We test our model on simulations that closely mimic the observed haplotypes and observe promising results.|
|Keywords:||Genographic Consortium; Chromosomes, Human, Y; Humans; DNA, Mitochondrial; Phylogeny; Recombination, Genetic; Haplotypes; Polymorphism, Single Nucleotide; Multigene Family; Algorithms; Models, Genetic|
|Description:||Copyright © Mary Ann Liebert, Inc. University of Adelaide consortium member: Alan Cooper|
|Appears in Collections:||Earth and Environmental Sciences publications|
Australian Centre for Ancient DNA publications
Environment Institute Leaders publications
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