Related papers: The disentangling number for phylogenetic mixtures
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
In the article 'Recursive queries on trees and data trees' (ICDT'13), Abiteboul et al., asked whether the containment problem for monadic datalog over unordered unranked labeled trees using the child relation and the descendant relation is…
Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
We study the problem of generating, ranking and unranking of unlabeled ordered trees whose nodes have maximum degree of $\Delta$. This class of trees represents a generalization of chemical trees. A chemical tree is an unlabeled tree in…
We prove that the isomorphism of scattered tree automatic linear orders as well as the existence of automorphisms of scattered word automatic linear orders are undecidable. For the existence of automatic automorphisms of word automatic…
A phylogenetic variety is an algebraic variety parameterized by a statistical model of the evolution of biological sequences along a tree. Understanding this variety is an important problem in the area of algebraic statistics with…
We study multicolour, oriented and high-dimensional discrepancies of the set of all subtrees of a tree. As our main result, we show that the $r$-colour discrepancy of the subtrees of any tree is a linear function of the number of leaves…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
A new tree model is introduced based on ordered trees, by distinguishing exactly one child of each node that \emph{has} children. The basic enumeration leads to a cubic equation of the generating function. The extraction of its coefficients…
Tanglegrams are drawings of two rooted binary phylogenetic trees and a matching between their leaf sets. The trees are drawn crossing-free on opposite sides with their leaf sets facing each other on two vertical lines. Instead of minimizing…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
We define a special case of tree decompositions for planar graphs that respect a given embedding of the graph. We study the analogous width of the resulting decomposition we call the embedded-width of a plane graph. We show both upper…
An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same…
A layerwise search in a split-by-edges tree (as defined by Br{\ae}ndeland, 2015) of agiven graph produces a maximum independent set in exponential time. A depth-first search produces an independent set, which may or may not be a maximum, in…