Related papers: Combinatorial Scoring of Phylogenetic Networks
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
Network models have been widely used to study diverse systems and analyze their dynamic behaviors. Given the structural variability of networks, an intriguing question arises: Can we infer the type of system represented by a network based…
Tree shape statistics quantify some aspect of the shape of a phylogenetic tree. They are commonly used to compare reconstructed trees to evolutionary models and to find evidence of tree reconstruction bias. Historically, to find a useful…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The…
Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Our work is motivated by and illustrated with application of association networks in computational biology, specifically in the context of gene/protein regulatory networks. Association networks represent systems of interacting elements,…
We present Collaborative Trees, a novel tree model designed for regression prediction, along with its bagging version, which aims to analyze complex statistical associations between features and uncover potential patterns inherent in the…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
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…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
A learning algorithm is presented which given the structure of a causal tree, will estimate its link probabilities by sequential measurements on the leaves only. Internal nodes of the tree represent conceptual (hidden) variables…
We present families of combinatorial classes described as trees with nodes that can carry one of two types of "flowers": integer partitions or integer compositions. Two parameters on the flowers of trees will be considered: the number of…