Related papers: Tropical Data Science
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
Phylogenetic trees in genetics and biology in general are all binary. We make an attempt to answer one fundamental question: Is such binary branching from the coarsest to the finest scales sustained by data? We convert this question into an…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of…
Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based)…
Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of…
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…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
Tropical geometry with the max-plus algebra has been applied to statistical learning models over tree spaces because geometry with the tropical metric over tree spaces has some nice properties such as convexity in terms of the tropical…