Reconstruction of Phylogenetic Networks

An algorithm for deconstructing and reconstructing Level-2 Binary Networks based on their distances

Bachelor thesis (2020)

Authors

R. Mol Electrical Engineering, Mathematics and Computer Science

Contributors

L.J.J. van Iersel Discrete Mathematics and Optimization - EEMCS (supervisor 1)
Yukihiro Murakami Discrete Mathematics and Optimization - EEMCS (coach)
E.M. van Elderen Mathematical Physics - EEMCS (supervisor 2)
Faculty
Electrical Engineering, Mathematics and Computer Science
Copyright: © 2020 Riche Mol
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Published Date

31-08-2020

Language

English

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Faculty

Electrical Engineering, Mathematics and Computer Science

Abstract

Van Iersel, Moulton, and Murakami (2020) proved that a level-2 binary phylogenetic network can be uniquely reconstructed based on the matrix of mulitsets of the distances of the leaves. Using a handful of lemma’s each
describing the steps of identifying cherries, uncontained leaves and blobs in the network, I created an algorithm for deconstruction the theoretical network corresponding to the matrix, and constructing the network based on the deconstruction steps. Unfortunately, this algorithm is not of polynomial time, as in the deconstruction programs are run that take time proportional to the sizes of the multisets of distances, which are upperbounded by 4n, where n is the number of leaves in the network. This algorithm is tested on more than 35000 networks with 10 to 24 leaves, and resulted in no errors.

Files

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