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PLG

Seminar

Exploring Treespace

St John, K (CUNY)
Monday 20 June 2011, 16:10-16:30

Seminar Room 1, Newton Institute

Abstract

Phylogenies, or evolutionary histories, play a central role in modern biology, illustrating the interrelationships between species, and also aiding the prediction of structural, physiological, and biochemical properties. The reconstruction of the underlying evolutionary history from a set of morphological characters or biomolecular sequences is difficult since the optimality criteria favored by biologists are NP-hard, and the space of possible answers is huge. The number of possible phylogenetic trees for n taxa is (2n − 5)!!. Due to the hardness and the large number of possible answers, clever searching techniques and heuristics are used to estimate the underlying tree. We explore the underlying space of trees, under different metrics, in particular the nearest-neighbor-interchange (NNI), subtree-prune-and-regraft (SPR), tree-bisection-and-reconnection (TBR), and Robinson-Foulds (RF) distances.

Presentation

[pdf ]

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