Polynomial-Time Algorithms for Phylogenetic Inference Problems

  title={Polynomial-Time Algorithms for Phylogenetic Inference Problems},
  author={Leo van Iersel and Remie Janssen and Mark Jones and Yukihiro Murakami and Norbert Zeh},
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… 
The rigid hybrid number for two phylogenetic trees
This paper characterize when two trees can be rigidly displayed by a certain type of phylogenetic network called a temporal tree-child network in terms of fork-picking sequences, and presents an infinite family of pairs of trees which demonstrates that the difference between the rigid hybrid number and the temporal-hybrid number for two phylogenetic trees on the same set of n leaves can grow at least linearly with n.
Weakly displaying trees in temporal tree-child network
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.
Heading in the right direction? Using head moves to traverse phylogenetic network space
It is proved that finding the shortest sequence of head moves between two networks is NP-hard and makes head moves a good candidate for local search heuristics.
Solving Phylogenetic Network Containment Problems using Cherry-picking Sequences
The tree-child sequences introduced by Linz and Semple characterize when a tree is embedded in a tree- Child network, and it is shown that this can be decided in linear time, and a linear time algorithm is provided for deciding whether two tree- child networks are isomorphic.


From Gene Trees to Species Trees
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.
A Reduction Algorithm for Computing The Hybridization Number of Two Trees
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.
Efficient Algorithms for Genomic Duplication Models
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.
On the Multiple Gene Duplication Problem
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].
Reconciliation with Non-Binary Species Trees
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.
Reconstruction of ancient molecular phylogeny.
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.
Linear-Time Algorithms for the Multiple Gene Duplication Problems
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.
Hybridization Number on Three Rooted Binary Trees is EPT
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.
Locating Multiple Gene Duplications through Reconciled Trees
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.