Related papers: Most Compact Parsimonious Trees
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
Hierarchical structure is ubiquitous in data across many domains. There are many hierarchical clustering methods, frequently used by domain experts, which strive to discover this structure. However, most of these methods limit discoverable…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
The recursive and hierarchical structure of full rooted trees is applicable to represent statistical models in various areas, such as data compression, image processing, and machine learning. In most of these cases, the full rooted tree is…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
To the known fact that Parsimony method sometimes fails on the problem of inferring species trees from gene trees, here we proved that no mater of what topology the true 9-taxon and greater species tree is the only thing one needs to break…
A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
Phylogenetic algebraic geometry is concerned with certain complex projective algebraic varieties derived from finite trees. Real positive points on these varieties represent probabilistic models of evolution. For small trees, we recover…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction…