# Cherry Picking: A Characterization of the Temporal Hybridization Number for a Set of Phylogenies

@article{Humphries2013CherryPA, title={Cherry Picking: A Characterization of the Temporal Hybridization Number for a Set of Phylogenies}, author={Peter J. Humphries and Simone Linz and Charles Semple}, journal={Bulletin of Mathematical Biology}, year={2013}, volume={75}, pages={1879-1890} }

Recently, we have shown that calculating the minimum–temporal-hybridization number for a set ${\mathcal{P}}$ of rooted binary phylogenetic trees is NP-hard and have characterized this minimum number when ${\mathcal{P}}$ consists of exactly two trees. In this paper, we give the first characterization of the problem for ${\mathcal{P}}$ being arbitrarily large. The characterization is in terms of cherries and the existence of a particular type of sequence. Furthermore, in an online appendix to the…

## 14 Citations

### Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies

- BiologyAdv. Appl. Math.
- 2019

### A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees

- Computer ScienceAlgorithmica
- 2022

We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations…

### Weakly displaying trees in temporal tree-child network

- BiologyArXiv
- 2020

This paper characterize when two trees can be rigidly displayed by a temporal tree-child network in terms of fork-picking sequences, a concept that is closely related to that of cherry- picking sequences.

### Deciding the existence of a cherry-picking sequence is hard on two trees

- BiologyDiscret. Appl. Math.
- 2019

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

- Computer ScienceAlgorithmica
- 2022

An algorithm for computing a tree-child network with temporal distance at most d and at most k reticulations in the jats:inline-formula, and the concept of <jats:italic>temporal distance, which is a measure for how close a tree -child network is to being temporal.

### Constructing Semi-Directed Level-1 Phylogenetic Networks from Quarnets

- Computer Science
- 2019

We introduce two algorithms for reconstructing semi-directed level-1 phylogenetic networks from their complete set of 4-leaf subnetworks, known as quarnets. The first algorithm, the sequential…

### Algorithms for Computational Biology: 7th International Conference, AlCoB 2020, Missoula, MT, USA, April 13–15, 2020, Proceedings

- EducationAlCoB
- 2020

Research, described in my Keynote lecture on folding genes at the 7th International Conference on Algorithms for Computational Biology (AlCoB 2020) in Missoula, Montana in April, blends computational mathematics, biology, chemistry, physics, computer science, and engineering in a creative way.

### Parameterized Algorithms in Bioinformatics: An Overview

- BiologyAlgorithms
- 2019

This work surveys recent developments of parameterized algorithms and complexity for important NP-hard problems in bioinformatics, and covers sequence assembly and analysis, genome comparison and completion, and haplotyping and phylogenetics.

## References

SHOWING 1-10 OF 25 REFERENCES

### Computing the Hybridization Number of Two Phylogenetic Trees Is Fixed-Parameter Tractable

- BiologyIEEE/ACM Transactions on Computational Biology and Bioinformatics
- 2007

This paper shows that the problem is fixed-parameter tractable in the two-tree instance when parameterized by this smallest number of reticulation vertices, which is NP-hard even when the collection consists of only two rooted binary phylogenetic trees.

### On the complexity of computing the temporal hybridization number for two phylogenies

- BiologyDiscret. Appl. Math.
- 2013

### Quantifying Hybridization in Realistic Time

- Computer ScienceJ. Comput. Biol.
- 2011

A new fixed-parameter algorithm for computing the minimum number of hybridization events for when two rooted binary phylogenetic trees are given is given, based on interleaving-a technique using repeated kernelization steps that are applied throughout the exhaustive search part of a fixed- parameter algorithm.

### Bounding the Number of Hybridisation Events for a Consistent Evolutionary History

- BiologyJournal of mathematical biology
- 2005

In this paper, the theoretical performance of some related bounds that result when merging pairs of trees into networks are described.

### A Survey of Combinatorial Methods for Phylogenetic Networks

- BiologyGenome biology and evolution
- 2011

This article gives an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation.

### A Simple Fixed Parameter Tractable Algorithm for Computing the Hybridization Number of Two (Not Necessarily Binary) Trees

- BiologyIEEE/ACM Transactions on Computational Biology and Bioinformatics
- 2013

Here, we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6rr!) · poly(n),…

### Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees

- Computer Science, BiologyISBRA
- 2010

Simulation results on biological and simulated datasets show that the new practical method presented is more efficient and robust than an existing method to compute the exact hybridization number.

### A First Step Toward Computing All Hybridization Networks For Two Rooted Binary Phylogenetic Trees

- Computer ScienceJ. Comput. Biol.
- 2012

This article presents the first algorithm--called ALLMAAFs--that calculates all maximum-acyclic-agreement forests for two rooted binary phylogenetic trees on the same set of taxa.

### Fixed-Parameter Algorithms in Phylogenetics

- Biology
- 2007

The use of fixed-parameter algorithms in the field of phylogenetics, which is the study of evolutionary relationships, is surveyed to find out how these algorithms have applications in seemingly unrelated areas such as genomic sequencing and finding and understanding genes.

### Analyzing and reconstructing reticulation networks under timing constraints

- Computer ScienceJournal of mathematical biology
- 2010

The first half of the paper shows that deciding whether a given number of additional taxa is sufficient to transform a non-temporal reticulation network into a temporal one is an NP-complete problem and provides an algorithm, called TemporalHybrid, for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists.