Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns
2008
Parida, L. | Mele, M. | Calafell, F. | Bertranpetit, J. | Schurr, T. | Santos, F. | Quintana-Murci, L. | Comas, D. | Tyler-Smith, C. | Zalloua, P. | Balanovska, E. | Balanovsky, O. | Behar, D. | Mitchell, R. | Jin, L. | Soodyall, H. | Pitchappan, R. | Cooper, A. | Royyuru, A. | Rosset, S. | et al. | Cooper, Alan
Copyright © Mary Ann Liebert, Inc. University of Adelaide consortium member: Alan Cooper
Show more [+] Less [-]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.
Show more [+] Less [-]Laxmi Parida, Marta Mele, Francesc Calafell, Jaume Bertranpetit and The Genographic Consortium
Show more [+] Less [-]AGROVOC Keywords
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