New FPT algorithms for finding the temporal hybridization number for sets of phylogenetic trees

New FPT algorithms for finding the temporal hybridization number for sets of phylogenetic trees

Borst, Sander (TU Delft Electrical Engineering, Mathematics and Computer Science)

van Iersel, Leo (mentor)

Delft University of Technology

2020-01-16

We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of t binary trees with n leaves each with a running time of O(5^k*n*m) where k is the minimum temporal hybridization number. We also present the concept of temporal distance, which is a measure for how close a tree-child network is to being temporal. Then we introduce an algorithm for computing a tree-child network with temporal distance at most p and at most k reticulations in O((8k)^p*5^k*n*m). Lastly, we introduce a O(6^k*k!*n) algorithm for computing a minimum temporal hybridization network for a set of two nonbinary trees.

Temporal network
Tree-child network
Phylogenetic network
Phylogenetics
Optimization
FPT Algorithm

http://resolver.tudelft.nl/uuid:2697da91-c596-48d1-9f09-f21da02ddb54

Student theses

master thesis

© 2020 Sander Borst