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searching for Distance matrix 55 found (113 total)

List of phylogenetics software (2,449 words) [view diff] exact match in snippet view article find links to article

(UPGMA), Bayesian phylogenetic inference, maximum likelihood, and distance matrix methods. List of phylogenetic tree visualization software Patterson

Complete-linkage clustering (2,170 words) [view diff] exact match in snippet view article find links to article

single-linkage clustering. The working example is based on a JC69 genetic distance matrix computed from the 5S ribosomal RNA sequence alignment of five bacteria:

Single-linkage clustering (2,496 words) [view diff] exact match in snippet view article find links to article

Else, go to step 2. This working example is based on a JC69 genetic distance matrix computed from the 5S ribosomal RNA sequence alignment of five bacteria:

U-matrix (220 words) [view diff] exact match in snippet view article find links to article

The U-matrix (unified distance matrix) is a representation of a self-organizing map (SOM) where the Euclidean distance between the codebook vectors of

Morphometrics (4,196 words) [view diff] no match in snippet view article find links to article

Morphometrics (from Greek μορΦή morphe, "shape, form", and -μετρία metria, "measurement") or morphometry refers to the quantitative analysis of form, a

Families of Structurally Similar Proteins database (232 words) [view diff] no match in snippet view article find links to article

database of structurally superimposed proteins generated using the "Distance-matrix ALIgnment" (DALI) algorithm.The database currently contains an extended

Computational phylogenetics (8,217 words) [view diff] no match in snippet view article find links to article

advent of phylogenomics, hundreds of genes may be analyzed at once. Distance-matrix methods of phylogenetic analysis explicitly rely on a measure of "genetic

Medoid (4,003 words) [view diff] exact match in snippet view article find links to article

out average dissimilarity with the mean of the dataset being used. A distance matrix is required for medoid-based clustering, which is generated using Jaccard

EMBOSS (324 words) [view diff] exact match in snippet view article find links to article

characters Phylogenetic discrete character methods Phylogeny distance matrix Phylogenetic distance matrix methods Phylogeny gene frequencies Phylogenetic gene

Wiener index (1,871 words) [view diff] exact match in snippet view article find links to article

topological indexes of chemical graphs, based on information in the distance matrix of the graph, have been developed subsequently to Wiener's work. The

Data Analytics Library (637 words) [view diff] exact match in snippet view article find links to article

change in another. Cosine distance matrix: Measuring pairwise distance using cosine distance. Correlation distance matrix: Measuring pairwise distance

Levenshtein distance (2,434 words) [view diff] exact match in snippet view article find links to article

Edit distance matrix for two words using cost of substitution as 1 and cost of deletion or insertion as 0.5

MAFFT (2,079 words) [view diff] exact match in snippet view article find links to article

is O(L^2) where L is the sequence. Distance Matrix – Using the calculated pairwise alignments, a distance matrix calculation is done to evaluate the

Tree alignment (2,313 words) [view diff] no match in snippet view article find links to article

In computational phylogenetics, tree alignment is a computational problem concerned with producing multiple sequence alignments, or alignments of three

Phoenix network coordinates (575 words) [view diff] exact match in snippet view article find links to article

internet distance matrix, i.e. for a system with N {\displaystyle N} internet nodes, the N × N {\displaystyle N\times N} internet distance matrix D can be

Molecular phylogenetics (2,164 words) [view diff] case mismatch in snippet view article find links to article

"Sequence Similarity Search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny Reconstruction". Protoc. Exch. doi:10.1038/protex.2013

Parallel all-pairs shortest path algorithm (3,034 words) [view diff] no match in snippet view article find links to article

it calculates shorter paths iterative. After |V | iterations the distance-matrix contains all the shortest paths. The following describes a sequential

Minimum evolution (2,437 words) [view diff] exact match in snippet view article find links to article

Neighbor joining also is a rather consistent method in that an input distance matrix with little to no errors will often provide an output tree with minimal

Primitive (phylogenetics) (1,068 words) [view diff] no match in snippet view article

reconciliation Probabilistic methods Maximum likelihood Bayesian inference Distance-matrix methods Neighbor-joining UPGMA Least squares Three-taxon analysis Current

Spectral shape analysis (1,488 words) [view diff] case mismatch in snippet view article find links to article

shapeDNA include singular values of Geodesic Distance Matrix (SD-GDM) and Reduced BiHarmonic Distance Matrix (R-BiHDM). However, the eigenvalues are global

Operation Virtual Shield (240 words) [view diff] case mismatch in snippet view article find links to article

the year 2016. Closed-circuit television Human Identification At a Distance MATRIX Total Information Awareness Gabriel Villa Schorn, Daniel (September

Phylogenetic tree (3,079 words) [view diff] no match in snippet view article find links to article

sequences are constructed using computational phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA, which calculate genetic

Phylogenetic signal (1,443 words) [view diff] no match in snippet view article find links to article

reconciliation Probabilistic methods Maximum likelihood Bayesian inference Distance-matrix methods Neighbor-joining UPGMA Least squares Three-taxon analysis Current

UniFrac (760 words) [view diff] exact match in snippet view article find links to article

the triangle inequality. If there are several different samples, a distance matrix can be created by making a tree for each pair of samples and calculating

Iterative Viterbi decoding (431 words) [view diff] exact match in snippet view article find links to article

input is placed in observation s[1..n], template t[1..m], // and [[distance matrix]] d[1..n,1..m] // remaining elements in matrices are solely for internal

BIRCH (2,275 words) [view diff] exact match in snippet view article find links to article

_{B}{\big \|}^{2}}}} These distances can also be used to initialize the distance matrix for hierarchical clustering, depending on the chosen linkage. For accurate

Maximum subarray problem (2,467 words) [view diff] exact match in snippet view article find links to article

a divide-and-conquer approach. Slightly faster algorithms based on distance matrix multiplication have been proposed by Tamaki & Tokuyama (1998) and by

Quadratic assignment problem (773 words) [view diff] exact match in snippet view article find links to article

{\displaystyle W} is the weight matrix and D {\displaystyle D} is the distance matrix. The problem is NP-hard, so there is no known algorithm for solving

Resistance distance (1,350 words) [view diff] exact match in snippet view article find links to article

J.; Lukovits, I.; Nikolic, S.; Trinajstic, N. (2002). "Resistance-distance matrix: a computational algorithm and its application". Int. J. Quantum Chem

ViennaRNA Package (801 words) [view diff] exact match in snippet view article find links to article

Program Description AnalyseDists Analyse a distance matrix AnalyseSeqs Analyse a set of sequences of common length Kinfold Simulate kinetic folding of

Sociomapping (1,013 words) [view diff] exact match in snippet view article find links to article

interpreted as distance, and 2) translating the multi-dimensional distance matrix into 2D coordinate system so that the correlation between map-distances

Floyd–Warshall algorithm (3,071 words) [view diff] exact match in snippet view article find links to article

3} are found. Finally, at k = 4, all shortest paths are found. The distance matrix at each iteration of k, with the updated distances in bold, will be:

DBSCAN (3,492 words) [view diff] exact match in snippet view article find links to article

\textstyle {\binom {n}{2}}} - n = (n²-n)/2-sized upper triangle of the distance matrix can be materialized to avoid distance recomputations, but this needs

Silhouette (clustering) (2,216 words) [view diff] exact match in snippet view article

needs pairwise distances and is typically implemented with a pairwise distance matrix. The O ( N 2 ) {\displaystyle {\mathcal {O}}(N^{2})} memory requirement

Graph realization problem (480 words) [view diff] case mismatch in snippet view article find links to article

Yichuan; Krislock, Nathan (2008), "Sensor Network Localization, Euclidean Distance Matrix Completions, and Graph Realization", Proceedings of the First ACM International

Nenad Trinajstić (801 words) [view diff] exact match in snippet view article find links to article

1063/1.430994. D. Bonchev; N. Trinajstić (1977). "Information theory, distance matrix, and molecular branching" (PDF). J. Chem. Phys. 67 (10): 4517. Bibcode:1977JChPh

Protein I-sites (694 words) [view diff] exact match in snippet view article find links to article

two peptide segments was evaluated using a combination of the RMS distance matrix error (dme): d m e = ∑ i = 1 L ∑ j = i − 5 i + 5 ( α i → j s 1 − α

Distance oracle (1,409 words) [view diff] exact match in snippet view article find links to article

special cases include: For k = 1 {\displaystyle k=1} we get the simple distance matrix. For k = 2 {\displaystyle k=2} we get a structure using O ( n 1.5 )

Phylogenetic inertia (867 words) [view diff] exact match in snippet view article find links to article

principal component analyses between species on a pairwise phylogenetic distance matrix. In another, different study, the authors described methods for measuring

Gamma distribution (9,096 words) [view diff] exact match in snippet view article find links to article

model among-sites rate variation when maximum likelihood, Bayesian, or distance matrix methods are used to estimate phylogenetic trees. Phylogenetic analyzes

Protein–protein interaction prediction (2,915 words) [view diff] exact match in snippet view article find links to article

16S rRNA sequences which they use as the canonical tree of life. The distance matrix constructed from this tree of life is then subtracted from the distance

Representative sequences (748 words) [view diff] exact match in snippet view article find links to article

orthologous family of representative sequences taken alone gives a distance matrix in close agreement with the consensus matrix. Protein sequences can

Albanian language (17,591 words) [view diff] no match in snippet view article find links to article

Matasovic, Ranko (2018). Page 35. Orel 2000, p. 191. "Excel File_Lexical-Distance-Matrix". Alternative Transport. 19 November 2016. "How much does language

Naqada culture (4,603 words) [view diff] exact match in snippet view article find links to article

across 7,400 years. Overall, the results showed that the biological distance matrix demonstrates the smallest biological distances, which indicate a closer

Low-rank approximation (3,884 words) [view diff] exact match in snippet view article find links to article

data matrix has missing values and the approximation is categorical. Distance matrix completion, in which case there is a positive definiteness constraint

SuperPose (625 words) [view diff] exact match in snippet view article find links to article

(b) a MolScript image, (c) a pairwise alignment, (d) a difference distance matrix and (e) the RMSD output for a pairwise superposition of 2TRX_A and

Didier Sornette (8,347 words) [view diff] exact match in snippet view article find links to article

structures between two time series. The method consists of constructing a distance matrix based on the matching of all sample data pairs between the two time

Structural alignment software (782 words) [view diff] case mismatch in snippet view article find links to article

Combinatorial Extension-Monte Carlo Cα Multi No server C. Guda 2004 DaliLite Distance Matrix Alignment C-Map Pair No server and download L. Holm 1993 TM-align TM-score

Quantitative comparative linguistics (7,824 words) [view diff] exact match in snippet view article find links to article

language comparisons. The input character matrix is used to compute the distance matrix either using the Hamming distance or the Levenshtein distance. The

Saccharibacteria (2,281 words) [view diff] exact match in snippet view article find links to article

using jsPhyloSVG, allows for quick access to GenBank sequences and distance matrix calculations between tree branches. Stable-isotope probing studies

Molecular Evolutionary Genetics Analysis (3,467 words) [view diff] exact match in snippet view article find links to article

properties of analysis results. It is a tool that may be used for distance matrix, phylogeny, tests, etc. within MEGA (megasoftware). MEGA's integrated

Multidimensional network (6,972 words) [view diff] exact match in snippet view article find links to article

layers, which is then exploited for its metric properties to build a distance matrix and hierarchically cluster the layers. Layers are successively aggregated

Matrix completion (6,062 words) [view diff] exact match in snippet view article find links to article

(4) full matrix completion. This method can be applied to Internet distance matrix completion and topology identification. Various matrix completion algorithms

Inferring horizontal gene transfer (8,981 words) [view diff] exact match in snippet view article find links to article

a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores". Journal of Bacteriology. 184

Multidimensional empirical mode decomposition (7,060 words) [view diff] exact match in snippet view article find links to article

put it into the corresponding resultant data matrix. Step 4 Form a distance matrix which the matrix elements are weighted by different distances between