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.
Original language | British English |
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Pages (from-to) | 1133-1154 |
Number of pages | 22 |
Journal | Journal of Computational Biology |
Volume | 15 |
Issue number | 9 |
DOIs | |
State | Published - 1 Nov 2008 |
Keywords
- ARG
- Gene clusters
- Genomic rearrangements
- Recombinations
- Strings