# Polynomial-Time Algorithms for Phylogenetic Inference Problems

@inproceedings{Iersel2018PolynomialTimeAF, title={Polynomial-Time Algorithms for Phylogenetic Inference Problems}, author={Leo van Iersel and Remie Janssen and Mark Jones and Yukihiro Murakami and Norbert Zeh}, booktitle={AlCoB}, year={2018} }

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model of speciation and duplication where duplications are clustered in duplication episodes. The goal is to minimize the number of such episodes. The second variant, Parental Hybridization, aims at inferring a species network based on a model of… Expand

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#### References

SHOWING 1-10 OF 36 REFERENCES

From Gene Trees to Species Trees

- Biology, Computer Science
- SIAM J. Comput.
- 2000

This paper studies various algorithmic issues in reconstructing a species tree from gene trees under the duplication and the mutation cost model and proposes a heuristic method that is significantly better than the existing program in Page's GeneTree 1.0 that starts the search from a random tree. Expand

Computing the minimum number of hybridization events for a consistent evolutionary history

- Computer Science, Mathematics
- Discret. Appl. Math.
- 2007

The main results of this paper show that computing this smallest number of hybridization events required to explain a given (input) set of data in a single (hybrid) phylogeny is APX- hard, and thus NP-hard, in the case the input is a collection of phylogenetic trees on sets of present-day species. Expand

A Reduction Algorithm for Computing The Hybridization Number of Two Trees

- Computer Science, Medicine
- Evolutionary bioinformatics online
- 2007

A new reduction-based algorithm for computing the minimum number of hybridization events, when the initial data set consists of two trees, which always gives the exact solution and runs efficiently on many real biological problems. Expand

Efficient Algorithms for Genomic Duplication Models

- Computer Science, Medicine
- IEEE/ACM Transactions on Computational Biology and Bioinformatics
- 2018

This work studies the method of clustering called minimum episodes for several models of allowed evolutionary scenarios with a focus on interval models in which every gene duplication has an interval consisting of allowed locations in the species tree. Expand

On the Multiple Gene Duplication Problem

- Computer Science
- ISAAC
- 1998

It is shown that the general form of this problem is NP-hard and various parameterized versions are hard for the complexity class W[1]. Expand

Reconciliation with non-binary species trees.

- Computer Science, Medicine
- Computational systems bioinformatics. Computational Systems Bioinformatics Conference
- 2007

This work presents the first formal algorithm for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model, and presents a dynamic programming algorithm for a combined loss model, in which losses in sibling species may be represented as a single loss in the common ancestor. Expand

Reconstruction of ancient molecular phylogeny.

- Biology, Medicine
- Molecular phylogenetics and evolution
- 1996

Under the assumption that differences among gene trees can be explained by gene duplications, and consequent losses, it is developed a method to obtain the global phylogeny minimizing the total number of postulated duplications and losses and to trace back such individual gene duplication to global genome duplications. Expand

Linear-Time Algorithms for the Multiple Gene Duplication Problems

- Biology, Medicine
- IEEE/ACM Transactions on Computational Biology and Bioinformatics
- 2011

Two variations of the MULTIPLE GENE DUPLICATION problems: the EPISODE-CLUSTERING (EC) problem and the MINIMUM EPISODES (ME) problem are studied and an optimal linear-time algorithm is proposed. Expand

Hybridization Number on Three Rooted Binary Trees is EPT

- Computer Science, Mathematics
- SIAM J. Discret. Math.
- 2016

The techniques generalize to more than three input trees with the exception of one key lemma that maps nodes in the network to tree nodes and, thus, minimizes the amount of guessing involved in constructing the network. Expand

Locating Multiple Gene Duplications through Reconciled Trees

- Biology, Computer Science
- RECOMB
- 2008

The first exact and efficient algorithm that determines a minimum number of locations for gene duplication events from the gene trees on the species tree is introduced, which can provide hypotheses for precise locations of large-scale gene duplication Events with data from relatively few gene trees. Expand