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Distance matrices are used in phylogeny as non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree (a phylogram , with informative branch lengths).
The Robinson–Foulds or symmetric difference metric, often abbreviated as the RF distance, is a simple way to calculate the distance between phylogenetic trees. [1]It is defined as (A + B) where A is the number of partitions of data implied by the first tree but not the second tree and B is the number of partitions of data implied by the second tree but not the first tree (although some ...
A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. [ 1 ] [ 2 ] In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon ...
Figure 1: Genetic distance map by Cavalli-Sforza et al. (1994) [1] Genetic distance is a measure of the genetic divergence between species or between populations within a species, whether the distance measures time from common ancestor or degree of differentiation. [2] Populations with many similar alleles have small genetic distances. This ...
Phenetics, popular in the mid-20th century but now largely obsolete, used distance matrix-based methods to construct trees based on overall similarity in morphology or similar observable traits (i.e. in the phenotype or the overall similarity of DNA, not the DNA sequence), which was often assumed to approximate phylogenetic relationships.
Distance methods attempt to construct an all-to-all matrix from the sequence query set describing the distance between each sequence pair. From this is constructed a phylogenetic tree that places closely related sequences under the same interior node and whose branch lengths closely reproduce the observed distances between sequences. Distance ...
UniFrac, a shortened version of unique fraction metric, is a distance metric used for comparing biological communities.It differs from dissimilarity measures such as Bray-Curtis dissimilarity in that it incorporates information on the relative relatedness of community members by incorporating phylogenetic distances between observed organisms in the computation.
The pair wise distance between sequences is calculated using Euclidean distance measure. The distance matrix thus obtained can be used to construct phylogenetic tree using clustering algorithms like neighbor-joining, UPGMA etc. A recent approach Pattern Extraction through Entropy Retrieval (PEER) provides direct detection of the k-mer length ...