Recombination and phylogeny: effects and detection

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Abstract
The role of phylogeny in guiding comparative studies is rapidly growing in the post genomic era. Most phylogeny reconstruction methods though, assume a single tree underlying a given alignment of sequences. However, when events such as recombination occur, different regions in the alignment may have different underlying trees. In this paper, we demonstrate via simulations, the effect of recombination on the accuracy of phylogeny reconstruction methods. Our results, coupled with the significance of recombination as an evolutionary mechanism, make it imperative to devise efficient and accurate methods for detecting recombination in sequence datasets. Hence, we introduce a simple, yet effective, method for detecting recombination in a given alignment, based on incongruence among phylogenetic trees in different regions of the alignment. We have studied the performance of our method on synthetic and biological datasets, and obtained good results.

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