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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).
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Automatic customization and visualization of phylogenetic trees iTOL - interactive Tree Of Life [6] annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface Microreact [7] Link, visualise and explore sequence and meta-data using phylogenetic trees, maps and timelines OneZoom [8]
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.
Edward Hitchcock's fold-out paleontological chart in his 1840 Elementary Geology. Although tree-like diagrams have long been used to organise knowledge, and although branching diagrams known as claves ("keys") were omnipresent in eighteenth-century natural history, it appears that the earliest tree diagram of natural order was the 1801 "Arbre botanique" (Botanical Tree) of the French ...
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.
Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, [4] the R-package, phangorn, [5] [6] and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as ...
Traditional single-gene studies are effective in establishing phylogenetic trees among closely related organisms, but have drawbacks when comparing more distantly related organisms or microorganisms. This is because of lateral gene transfer, convergence, and varying rates of evolution for different genes. By using entire genomes in these ...