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Finding the tree and branch lengths minimizing the least squares residual is an NP-complete problem. [2] However, for a given tree, the optimal branch lengths can be determined in () time for ordinary least squares, () time for weighted least squares, and () time for generalised least squares (given the inverse of the covariance matrix).
Phylogenetic diversity is a measure of biodiversity which incorporates phylogenetic difference between species. It is defined and calculated as "the sum of the lengths of all those branches that are members of the corresponding minimum spanning path ", [1] in which 'branch' is a segment of a cladogram, and the minimum spanning path is the ...
In phylogenetics and computational phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes (or minimizes the cost of differentially weighted character-state changes). Under the maximum-parsimony criterion, the optimal tree will minimize the amount ...
Computational phylogenetics. Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, heuristics, and approaches involved in phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa.
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.
In mathematics and phylogenetics, Newick tree format (or Newick notation or New Hampshire tree format) is a way of representing graph-theoretical trees with edge lengths using parentheses and commas. It was adopted by James Archie, William H. E. Day, Joseph Felsenstein, Wayne Maddison, Christopher Meacham, F. James Rohlf, and David Swofford, at ...
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 ...
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 ...