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J Comput Biol. 2008 Nov;15(9):1133-54. doi: 10.1089/cmb.2008.0065.

Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns.

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Computational Biology Center, IBM TJ Watson Research, Yorktown Heights, NY 10598, USA.


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.

[Indexed for MEDLINE]

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