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Phylogenetic trees generated by computational phylogenetics can be either rooted or unrooted depending on the input data and the algorithm used. A rooted tree is a directed graph that explicitly identifies a most recent common ancestor (MRCA), [citation needed] usually an inputed sequence that is not represented in the input.
A phylogenetic analysis typically consists of five major steps. The first stage comprises sequence acquisition. The following step consists of performing a multiple sequence alignment, which is the fundamental basis of constructing a phylogenetic tree. The third stage includes different models of DNA and amino acid substitution.
One use of phylogenetic analysis involves the pharmacological examination of closely related groups of organisms. Advances in cladistics analysis through faster computer programs and improved molecular techniques have increased the precision of phylogenetic determination, allowing for the identification of species with pharmacological potential.
The term monophyly, or monophyletic, derives from the two Ancient Greek words μόνος (mónos), meaning "alone, only, unique", and φῦλον (phûlon), meaning "genus, species", [4] [5] and refers to the fact that a monophyletic group includes organisms (e.g., genera, species) consisting of all the descendants of a unique common ancestor.
A lineage is a single line of descent or linear chain within the tree, while a clade is a (usually branched) monophyletic group, containing a single ancestor and all its descendants. [3] Phylogenetic trees are typically created from DNA, RNA or protein sequence data. Apart from this, morphological differences and similarities have been, and ...
No system of nomenclature attempts to name every clade; this would be particularly difficult with traditional nomenclature since every named taxon must be given a lower rank than any named taxon in which it is nested, so the number of names that can be assigned in a nested set of taxa can be no greater than the number of generally recognized ranks.
The idea of a tree of life arose from ancient notions of a ladder-like progression from lower into higher forms of life (such as in the Great Chain of Being).Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book Elementary Geology, by Edward Hitchcock (first edition: 1840).
Willi Hennig 1972 Peter Chalmers Mitchell in 1920 Robert John Tillyard. The original methods used in cladistic analysis and the school of taxonomy derived from the work of the German entomologist Willi Hennig, who referred to it as phylogenetic systematics (also the title of his 1966 book); but the terms "cladistics" and "clade" were popularized by other researchers.