Reconstruction of Phylogenetic Networks

Reconstruction of Phylogenetic Networks: An algorithm for deconstructing and reconstructing Level-2 Binary Networks based on their distances

Mol, Riche (TU Delft Electrical Engineering, Mathematics and Computer Science)

van Iersel, L.J.J. (mentor)
Murakami, Yukihiro (graduation committee)
van Elderen, E.M. (graduation committee)

Delft University of Technology

2020-08-31

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.

http://resolver.tudelft.nl/uuid:7b0f3919-0e78-4264-9e8f-028cf3fcde31

Student theses

bachelor thesis

© 2020 Riche Mol