Results 11 to 20 of about 149,599 (256)

A vector representation for phylogenetic trees. [PDF]

Philos Trans R Soc Lond B Biol Sci
Good representations for phylogenetic trees and networks are important for enhancing storage efficiency and scalability for the inference and analysis of evolutionary trees for genes, genomes and species. We propose a new representation for rooted phylogenetic trees that encodes a tree on n
Chauve C, Colijn C, Zhang L.
europepmc   +4 more sources

Phylogenetic trees [PDF]

Journal of Software for Algebra and Geometry, 2021
We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for ...
Baños, Hector, Bushek, Nathaniel, Davidson, Ruth, Gross, Elizabeth, Harris, Pamela E., Krone, Robert, Long, Colby, Stewart, Allen, Walker, Robert   +8 more
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tidy tree: A New Layout for Phylogenetic Trees. [PDF]

Mol Biol Evol, 2022
AbstractMany layouts exist for visualizing phylogenetic trees, allowing to display the same information (evolutionary relationships) in different ways. For large phylogenies, the choice of the layout is a key element, because the printable area is limited, and because interactive on-screen visualizers can lead to unreadable phylogenetic relationships ...
Penel S, de Vienne DM.
europepmc   +4 more sources

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

The Shapley value of phylogenetic trees [PDF]

Journal of Mathematical Biology, 2007
References added, and a section (calculating the Shapley value of a tree game from its subtrees) was removed for length reasons (request of referee) and may appear in another paper. 16 pages; related work at http://www.math.hmc.edu/~su/papers.html. Journal of Mathematical Biology, to appear.
Haake, Claus-Jochen, Kashiwada, Akemi, Su, Francis Edward   +2 more
openaire   +6 more sources

Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences. [PDF]

PLoS ONE, 2013
Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited.
Soichirou Satoh, Mamoru Mimuro, Ayumi Tanaka   +2 more
doaj   +1 more source

DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees

Brazilian Journal of Biology, 2023
This study introduces a new method to construct phylogenetic trees by combining both of the Simple Sequence Repeats (SSRs) and sequence alignments.
M. Alhawatema
doaj   +1 more source

Characterization of a Branch of the Phylogenetic Tree [PDF]

Journal of Theoretical Biology, 2003
We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there should be a ``tortoise and hare effect'': Those genera with the smallest species death rate are likely to survive much
Samuel, Stuart A., Weng, Gezhi
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All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees

Algorithms for Molecular Biology, 2023
Objective In mathematical phylogenetics, a labeled rooted binary tree topology can possess any of a number of labeled histories, each of which represents a possible temporal ordering of its coalescences.
Shaili Mathur, Noah A. Rosenberg
doaj   +1 more source

Operads and phylogenetic trees

Theory and Applications of Categories, 2017
We construct an operad $\mathrm{Phyl}$ whose operations are the edge-labelled trees used in phylogenetics. This operad is the coproduct of $\mathrm{Com}$, the operad for commutative semigroups, and $[0,\infty)$, the operad with unary operations corresponding to nonnegative real numbers, where composition is addition.
Baez, JC, Otter, N
openaire   +4 more sources