UPGMA (unweighted pair group method with arithmetic mean) is a simple agglomerative (bottom-up) hierarchical clustering method. It also has a weighted...
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Distance matrix (section UPGMA)
based methods for phylogeny reconstruction: Additive tree reconstruction UPGMA Neighbor joining Fitch–Margoliash Additive tree reconstruction is based...
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Minimum evolution (section UPGMA)
similarly powerful but overall much more complicated compared to UPGMA and other options. UPGMA is a clustering method. It builds a collection of clusters that...
20 KB (2,446 words) - 03:42, 30 June 2025
The guide tree in the initial versions of Clustal was constructed via a UPGMA cluster analysis of the pairwise alignments, hence the name CLUSTAL.cf....
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taxa ( a {\displaystyle a} to e {\displaystyle e} ) have been clustered by UPGMA based on a matrix of genetic distances. The matrix is showed as a heatmap...
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constant rate of evolution (i.e., a molecular clock) across lineages. The UPGMA (Unweighted Pair Group Method with Arithmetic mean) and WPGMA (Weighted...
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tree-building methods include unweighted pair group method using arithmetic mean (UPGMA) and Neighbor joining, which are distance-based methods, Maximum parsimony...
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Computational phylogenetics (section UPGMA and WPGMA)
local high-variation regions that appear across multiple subtrees. The UPGMA (Unweighted Pair Group Method with Arithmetic mean) and WPGMA (Weighted...
65 KB (8,217 words) - 01:14, 29 April 2025
and Michener. The WPGMA method is similar to its unweighted variant, the UPGMA method. The WPGMA algorithm constructs a rooted tree (dendrogram) that reflects...
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Quantitative comparative linguistics (section UPGMA)
Indo-European database. The methods compared were UPGMA, NJ MP, MC, WMC and GA. The PAUP software package was used for UPGMA, NJ, and MC as well as computing the majority...
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referred to as parsimony), unweighted pair group method with arithmetic mean (UPGMA), Bayesian phylogenetic inference, maximum likelihood, and distance matrix...
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phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA, which calculate genetic distance from multiple sequence alignments, are...
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schemes include complete linkage clustering, average linkage clustering (UPGMA and WPGMA), and Ward's method. In the naive algorithm for agglomerative...
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joining will reconstruct the true tree with high probability. Compared with UPGMA and WPGMA, neighbor joining has the advantage that it does not assume all...
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source No Linux, Mac OS (homebrew) Official website Base-By-Base No MUSCLE UPGMA, NJ, complete and single linkages, WPMGA Visual summary, percent identity...
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likelihood Bayesian inference Distance-matrix methods Neighbor-joining UPGMA Least squares Three-taxon analysis Current topics PhyloCode DNA barcoding...
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elements of each cluster (also called average linkage clustering, used e.g. in UPGMA): 1 | A | ⋅ | B | ∑ x ∈ A ∑ y ∈ B d ( x , y ) . {\displaystyle {1 \over...
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distances), complete linkage clustering (the maximum of object distances), and UPGMA or WPGMA ("Unweighted or Weighted Pair Group Method with Arithmetic Mean"...
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Hierarchical clustering Molecular clock Neighbor-joining Single-linkage clustering UPGMA WPGMA Sorensen T (1948). "A method of establishing groups of equal amplitude...
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by signed reversals: an algorithm for understanding genomic evolution. UPGMA: a distance-based phylogenetic tree construction algorithm. Velvet: a set...
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phylogenetic tree construction, ultrametric distances are also utilized by the UPGMA and WPGMA methods. These algorithms require a constant-rate assumption and...
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cladograms but are not cladograms. For example, phenetic algorithms, such as UPGMA and Neighbor-Joining, group by overall similarity, and treat both synapomorphies...
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occurring early on). Sibley and Ahlquist's DNA-DNA hybridization studies and UPGMA tree published in 1990 supported brown pelican as sister to a clade comprising...
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Genetic analysis by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) revealed several clusters irrespective of geographical origin. Before synthetic...
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distance for every pair of input sequences to create a distance matrix. UPGMA clusters the distance matrix to produce a binary tree. From this tree a...
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the mBed and k-means methods. A guide tree is then constructed using the UPGMA method that is used by the HH align package. This guide tree is used to...
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and open reading frames (ORFs) analysis. Phylogenetic tree construction UPGMA, Neighbour joining with bootstrapping and consensus trees Online Database...
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American species based on amplified fragment length polymorphism data (UPGMA). SY22, ST23, and M70 are A. gallica specimens collected from Michigan,...
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Correspondence between HAC linkages and BIRCH distances HAC Linkage BIRCH distance UPGMA D2² WPGMA D0² Ward 2 D4²...
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cladistic analysis of all 15 taxa then known to produce glucosinolates. In UPGMA phenograms, Limnanthaceae clustered with Balsaminaceae. Similarly, cladistic...
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