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In computational phylogenetics, tree alignment is a computational problem concerned with producing multiple sequence alignments, or alignments of three or more sequences of DNA, RNA, or protein. Sequences are arranged into a phylogenetic tree , modeling the evolutionary relationships between species or taxa .
Least squares distance tree construction aims to find the tree (topology and branch lengths) with minimal S. This is a non-trivial problem. It involves searching the discrete space of unrooted binary tree topologies whose size is exponential in the number of leaves. For n leaves there are 1 • 3 • 5 • ... • (2n-3) different topologies.
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 ...
In biology, phylogenetics (/ ˌ f aɪ l oʊ dʒ ə ˈ n ɛ t ɪ k s,-l ə-/) [1] [2] [3] is the study of the evolutionary history of life using genetics, which is known as phylogenetic inference. It establishes the relationship between organisms with the empirical data and observed heritable traits of DNA sequences, protein amino acid sequences ...
The uncertainty of any inferred phylogenetic tree based on a single gene can be resolved by using several common genes or even evidence from whole genomes. [12] One such approach, sometimes called 'multi-locus typing', has been used to deduce phylogenic trees for organisms that exchange genes, such as meningitis bacteria.
In practice the distance matrix rarely satisfies this condition, but neighbor joining often constructs the correct tree topology anyway. [8] The correctness of neighbor joining for nearly additive distance matrices implies that it is statistically consistent under many models of evolution; given data of sufficient length, neighbor joining will ...
Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship (shared descent), progenitor-descendant relationship (serial descent), and degree of evolutionary change.
Phylogenomics is the intersection of the fields of evolution and genomics. [1] The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. [2] It is a group of techniques within the larger fields of phylogenetics and genomics.