Related papers: Not all phylogenetic networks are leaf-reconstruct…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…
Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
In evolutionary biology, phylogenetic networks are now widely used to represent the historical relationships between species and population, when this history includes reticulation events such as hybridization, gene flow and admixture…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
A normal (phylogenetic) network with $k$ reticulations displays $2^k$ phylogenetic trees. In this paper, we establish an analogous result for tree-child (phylogenetic) networks with no underlying $3$-cycles. In particular, we show that a…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
The tree-metric theorem provides a necessary and sufficient condition for a dissimilarity matrix to be a tree metric, and has served as the foundation for numerous distance-based reconstruction methods in phylogenetics. Our main result is…