Results 31 to 40 of about 2,045,161 (322)
Matchings and phylogenetic trees [PDF]
Proceedings of the National Academy of Sciences, 1998 This paper presents a natural coordinate system for phylogenetic trees using a correspondence with the set of perfect matchings in the complete graph. This correspondence produces a distance between phylogenetic trees, and a way of enumerating all trees in a minimal step order. It is useful in randomized algorithms because it enables moves on the space
Diaconis, Persi W., Holmes, Susan P.
openaire +2 more sources
PhySortR: a fast, flexible tool for sorting phylogenetic trees in R [PDF]
PeerJ, 2016 A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we
Timothy G. Stephens +3 more
doaj +2 more sources
Unrealistic phylogenetic trees may improve phylogenetic footprinting [PDF]
Bioinformatics, 2017 Abstract Motivation The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole.
Nettling, Martin +3 more
openaire +3 more sources
A Note on Encodings of Phylogenetic Networks of Bounded Level [PDF]
, 2009 Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks
A Batbedat +30 more
core +4 more sources
Tree-Based Unrooted Phylogenetic Networks [PDF]
Bulletin of Mathematical Biology, 2017 Abstract Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph
Francis, Andrew +2 more
openaire +5 more sources
Information theoretic generalized Robinson-Foulds metrics for comparing phylogenetic trees
Bioinform., 2020 MOTIVATION The Robinson-Foulds (RF) metric is widely used by biologists, linguists and chemists to quantify similarity between pairs of phylogenetic trees.
Martin R. Smith
semanticscholar +1 more source
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees [PDF]
PLoS ONE, 2014 A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees.
D. Rabosky
semanticscholar +1 more source
Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data [PDF]
, 2014 1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity.
Barraclough, Timothy G +4 more
core +2 more sources
Nonbinary Tree-Based Phylogenetic Networks [PDF]
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018 Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example represent gene transfer events.
Laura Jetten, Leo van Iersel
openaire +5 more sources
Iroki: automatic customization and visualization of phylogenetic trees
PeerJ, 2020 Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in ...
Ryan M. Moore +4 more
semanticscholar +1 more source