RJ
R. Janssen
info
Please Note
<p>This page displays the records of the person named above and is not linked to a unique person identifier. This record may need to be merged to a profile.</p>
1 records found
1
Bachelor thesis
(2019)
-
Robbert Huijsman, Leo van Iersel, Yuki Murakami, Remie Janssen, Bart van den Dries
Interest in phylogenetic trees for histories of species and DNA has spawned many problems, one of which is TreeContainment; a problem that asks whether a tree is contained within a network. The TreeContainment problem is proven to be NP-hard for general trees and networks, however it is solvable in polynomial time for networks that meet the tree-child restriction. An algorithm to solve TreeContainment for binary tree-child networks has been created previously with quadratic running time (van Iersel, Semple, Steel, 2010). Janssen and Murakami have recently created a new algorithm that solves a larger problem NetworkContainment, for semi-binary tree-child networks (Janssen, Murakami, 2019). This new algorithm uses tree-child sequences introduced by Linz and Semple, but there has not been an implementation of it until now. In this paper I show an implementation (using Python) of this algorithm, in which I have made a modification that increases its speed on networks with large indegrees. Furthermore I have proven in this paper that the output of this algorithm remains correct under this modification, and that the running time of the modified algorithm is now linear without requiring a constant maximum indegree at all.
...
Interest in phylogenetic trees for histories of species and DNA has spawned many problems, one of which is TreeContainment; a problem that asks whether a tree is contained within a network. The TreeContainment problem is proven to be NP-hard for general trees and networks, however it is solvable in polynomial time for networks that meet the tree-child restriction. An algorithm to solve TreeContainment for binary tree-child networks has been created previously with quadratic running time (van Iersel, Semple, Steel, 2010). Janssen and Murakami have recently created a new algorithm that solves a larger problem NetworkContainment, for semi-binary tree-child networks (Janssen, Murakami, 2019). This new algorithm uses tree-child sequences introduced by Linz and Semple, but there has not been an implementation of it until now. In this paper I show an implementation (using Python) of this algorithm, in which I have made a modification that increases its speed on networks with large indegrees. Furthermore I have proven in this paper that the output of this algorithm remains correct under this modification, and that the running time of the modified algorithm is now linear without requiring a constant maximum indegree at all.