Related papers: Constructing a Minimum-Level Phylogenetic Network …
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…
Consider a set of labels $L$ and a set of trees ${\mathcal T} = \{{\mathcal T}^{(1), {\mathcal T}^{(2), ..., {\mathcal T}^{(k) \$ where each tree ${\mathcal T}^{(i)$ is distinctly leaf-labeled by some subset of $L$. One fundamental problem…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
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…
The three-in-a-tree problem asks for an induced tree of the input graph containing three mandatory vertices. In 2006, Chudnovsky and Seymour [Combinatorica, 2010] presented the first polynomial time algorithm for this problem, which has…
Semi-directed networks are partially directed graphs that model evolution where the directed edges represent reticulate evolutionary events. We present an algorithm that reconstructs binary $n$-leaf semi-directed level-1 networks in $O(…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the…
We study the problem of finding small trees. Classical network design problems are considered with the additional constraint that only a specified number $k$ of nodes are required to be connected in the solution. A prototypical example is…
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…
Let $n\geq 3$ and $r_n$ be a $3$-polytopal graph such that for every $3\leq i\leq n$, $r_n$ has at least one vertex of degree $i$. We find the minimal vertex count for $r_n$. We then describe an algorithm to construct the graphs $r_n$. A…
Phylogenetic networks represent evolutionary histories of sets of taxa where horizontal evolution or hybridization has occurred. Placing a Markov model of evolution on a phylogenetic network gives a model that is particularly amenable to…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
Analyzing relational data consisting of multiple samples or layers involves critical challenges: How many networks are required to capture the variety of structures in the data? And what are the structures of these representative networks?…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…