Distance matrices are used in phylogeny as non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances...

tree reconstruction is based on additive and ultrametric distance matrices. These matrices have a special characteristic: Consider an additive matrix...

due to a similar need to deal with large amounts of data. Distance matrices in phylogeny Folk taxonomy Form classification Linnaean taxonomy Phenomics...

individual observations all plotted at zero height). Cladogram Distance matrices in phylogeny Hierarchical clustering MEGA, a freeware for drawing dendrograms...

topology anyway. The correctness of neighbor joining for nearly additive distance matrices implies that it is statistically consistent under many models of evolution;...

(BLOck SUbstitution Matrix) series of matrices rectifies this problem. Henikoff & Henikoff constructed these matrices using multiple alignments of evolutionarily...

of perfect phylogeny. In general there are two different data types that are used in the construction of a phylogenetic tree. In distance-based computations...

refers to the evolutionary distance; greater numbers correspond to greater distances. Matrices using greater evolutionary distances are extrapolated from those...

phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, heuristics, and approaches involved in phylogenetic...

evolution is a distance method employed in phylogenetics modeling. It shares with maximum parsimony the aspect of searching for the phylogeny that has the...

molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters. Each program is controlled through a menu...

reconstructing phylogenetic trees from a distance matrix containing missing values, i.e. incomplete matrices, are available: Triangles method by Guénoche...

inference – Statistical method for molecular phylogenetics Distance matrices in phylogeny – Matrices used in construction of phylogenetic trees Neighbor joining –...

maximum likelihood estimation of phylogeny as well as Bayesian inference in phylogeny. Estimates of evolutionary distances (numbers of substitutions that...

data matrices become larger, branch support values often continue to increase as bootstrap values plateau at 100%. Thus, for large data matrices, branch...

Least squares inference in phylogeny generates a phylogenetic tree based on an observed matrix of pairwise genetic distances and optionally a weight matrix...

BLOSUM-62 matrix is one of the best substitution matrices for detecting weak protein similarities. BLOSUM matrices with high numbers are designed for comparing...

Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenies include neighbor-joining, maximum...

nucleotide composition of each position in the putative motif. The alignment can then be refined using these matrices. In standard profile analysis, the matrix...

In geometry, the geometric median of a discrete point set in a Euclidean space is the point minimizing the sum of distances to the sample points. This...

descriptions of rate matrices on this page accurately reflect the relative magnitude of different substitutions, but these rate matrices are not scaled such...

substitution matrices that reflect the probabilities of given character-to-character substitutions. A series of matrices called PAM matrices (Point Accepted...

Analysis (MSSA), Distance Fit (DFIT) and Quartet Fit (QFIT), implemented in the software CLANN. Supertrees have been applied to produce phylogenies of many groups...

to shape viral phylogenies. Since the term was coined in 2004, research on viral phylodynamics has focused on transmission dynamics in an effort to shed...

e., an edge that connects two vertices that are an odd distance (>1) apart from each other in the cycle. Strongly chordal graphs have a forbidden subgraph...

1137/11085390X, S2CID 934546. Fulkerson, D. R.; Gross, O. A. (1965), "Incidence matrices and interval graphs", Pacific J. Math., 15 (3): 835–855, doi:10.2140/pjm...

in this way, T is called a k-leaf root of G. A graph is a leaf power if it is a k-leaf power for some k. These graphs have applications in phylogeny,...

Zibrowius, H. (1999). "Biochemical markers of zooxanthellae symbiosis in soluble matrices of skeleton of 24 Scleractinia species". Comparative Biochemistry...

parsimonious models based on the eigenvalue decomposition of the covariance matrices, that provide a balance between overfitting and fidelity to the data. One...

provides a much wider range of scoring matrices, making it easier to tailor a search to a specific evolutionary distance. An extremely fast but considerably...