Related papers: Level-1 Phylogenetic Networks and their Balanced M…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…
Many biological networks grow by elongation of filaments that can branch and fuse -- typical examples include fungal mycelium or slime mold. These networks must simultaneously perform multiple tasks such as transport, exploration, and…
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…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…
A phylogenetic tree is an edge-weighted binary tree, with leaves labelled by a collection of species, that represents the evolutionary relationships between those species. For such a tree, a phylogenetic diversity index is a function that…
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…
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…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
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…
A recurring theme in the least squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least squares estimates of edge lengths. These formulas have proved useful for the development of efficient…
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Least squares estimation of phylogenies is an established family of methods with good statistical properties. State-of-the-art least squares phylogenetic estimation proceeds by first estimating a distance matrix, which is then used to…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
Phylogenetic networks can model more complicated evolutionary phenomena that trees fail to capture such as horizontal gene transfer and hybridization. The same Markov models that are used to model evolution on trees can also be extended to…