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SplitsTree
SplitsTree is a freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, split graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees. Software SplitsTree implements published methods such as split (phylogenetics), split decomposition, neighbor-net, consensus networks, super networks methods or methods for computing Hybrid (biology), hybridization or simple genetic recombination, recombination networks. It uses the Nexus file, NEXUS file format. The splits graph is defined using a special data block (SPLITS block). See also *Phylogenetic tree viewers *Dendroscope *MEGAN References {{Reflist External links SplitsTree homepage(New Website for informations about SplitsTree)for the latest version (4.15) and manual (June 2019), hosted by thDepartment of Computer Scienceat the University of Tübingen, Eberhard Karls University TübingenAlgorithms in Bioinformatics Daniel Huson's working group deve ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Network
A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes (nodes with two parents) instead of only tree nodes (a hierarchy of nodes, each with only one parent). Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, the R-package, phangorn, and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees. Many kinds and subclasses of phylogenetic networks have bee ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Split (phylogenetics)
A split in phylogenetics is a bipartition of a set of taxa, and the smallest unit of information in unrooted phylogenetic tree A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...s: each edge of an unrooted phylogenetic tree represents one split, and the tree can be efficiently reconstructed from its set of splits. Moreover, when given several trees, the splits occurring in more than half of these trees give rise to a consensus tree, and the splits occurring in a smaller fraction of the trees generally give rise to a consensus split network. Pairs of splits are ''compatible'' if any of the subsets defined by each split do not overlap. See also * SplitsTree, a program for inferring phylogenetic (split) networks. References Phylogenetics Trees (data structures) {{geneti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Neighbor-net
NeighborNet is an algorithm for constructing phylogenetic networks which is loosely based on the neighbor joining algorithm. Like neighbor joining, the method takes a distance matrix as input, and works by agglomerating clusters. However, the NeighborNet algorithm can lead to collections of clusters which overlap and do not form a hierarchy, and are represented using a type of phylogenetic network called a splits graph. If the distance matrix satisfies the Kalmanson combinatorial conditions then Neighbor-net will return the corresponding circular ordering. The method is implemented in the SplitsTree and R/Phangorn packages. Examples of the application of Neighbor-net can be found in virology, horticulture, dinosaur genetics, comparative linguistics Comparative linguistics is a branch of historical linguistics that is concerned with comparing languages to establish their historical relatedness. Genetic relatedness implies a common origin or proto-language and comparative ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dendroscope
Dendroscope is an interactive computer software program written in Java for viewing Phylogenetic trees. This program is designed to view trees of all sizes and is very useful for creating figures. Dendroscope can be used for a variety of analyses of molecular data sets but is particularly designed for metagenomics or analyses of uncultured environmental samples. It was developed by Daniel Huson and his colleagues at the University of Tübingen in Germany, who also created SplitsTree. See also *List of phylogenetic tree visualization software *SplitsTree *MEGAN Megan is a Welsh feminine given name, originally a diminutive form of Margaret. Margaret is from the Greek μαργαρίτης (''margarítēs''), Latin ''margarīta'', "pearl". Megan is one of the most popular Welsh-language names for women in ... References External links Dendroscope homepage hosted at the University of Washington Phylogenetics software {{science-software-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nexus File
The extensible NEXUS file format is widely used in phylogenetics, evolutionary biology, and bioinformatics. It stores information about taxa In biology, a taxon (back-formation from ''taxonomy''; : taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and ..., morphological character states, DNA and protein sequence alignments, distances, and phylogenetic trees. The NEXUS format also allows the storage of data that can facilitate analyses, such as sets of characters or taxa. Many popular phylogenetic programs, including PAUP*,PAUP* — Phylogenetic Analysis Using Parsimony *and other methods [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Tree Viewers
OneZoom This list of phylogenetic tree viewing software is a compilation of software tools and web portals used in visualizing phylogenetic trees. Online software Desktop software 1 "All" refers to Microsoft Windows, Apple OSX and Linux; L=Linux, M=Apple Mac, W=Microsoft Windows Libraries See also * List of phylogenetics software * Phylogenetics References {{reflist External links A 'comprehensive list' of Tree Editors Genetics databases phylog phylogenetics In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ... Phylogenetics Visualization software Tree of life (biology) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MEGAN
Megan is a Welsh feminine given name, originally a diminutive form of Margaret. Margaret is from the Greek μαργαρίτης (''margarítēs''), Latin ''margarīta'', "pearl". Megan is one of the most popular Welsh-language names for women in Wales and England, and is commonly truncated to Meg. Megan was one of the most popular feminine names in the English-speaking world in the 1990s, peaking in 1990 in the United States and 1999 in the United Kingdom. Approximately 54% of people named Megan born in the US were born in 1990 or later. The name is also frequently spelled Meagan, Meaghan, Meghan, or Mehgan outside of Wales and the rest of the United Kingdom due to spelling influence from Irish-language names Meagan * Meagan Best (born 2002), Barbadian squash player * Meagan Chauke (born 1992), South African activist * Meagan Cignoli, American photographer, filmmaker, and businessperson * Meagan Day, American writer, editor, and activist * Meagan Dixon (born 1997), Austr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Recombination
Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) ''interchromosomal'' recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes (random orientation of pairs of homologous chromosomes in meiosis I); & (2) ''intrachromosomal'' recombination, occurring through crossing over. During meiosis in eukaryotes, genetic recombination involves the pairing of homologous chromosomes. This may be followed by information transfer between the chromosomes. The information transfer may occur without physical exchange (a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hybrid (biology)
In biology, a hybrid is the offspring resulting from combining the qualities of two organisms of different varieties, subspecies, species or genera through sexual reproduction. Generally, it means that each cell has genetic material from two different organisms, whereas an individual where some cells are derived from a different organism is called a chimera. Hybrids are not always intermediates between their parents such as in blending inheritance (a now discredited theory in modern genetics by particulate inheritance), but can show hybrid vigor, sometimes growing larger or taller than either parent. The concept of a hybrid is interpreted differently in animal and plant breeding, where there is interest in the individual parentage. In genetics, attention is focused on the numbers of chromosomes. In taxonomy, a key question is how closely related the parent species are. Species are reproductively isolated by strong barriers to hybridization, which include genetic and morph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heterobranchia Tree
Heterobranchia, the heterobranchs (meaning "different gill"), is a taxonomic clade of snails and slugs, which includes marine, aquatic, and terrestrial gastropod molluscs. Heterobranchia is one of the main clades of gastropods. Currently Heterobranchia comprises two groups: the opisthobranchs, and the pulmonates. Diversity The two subdivisions of this large clade are quite diverse: * Opisthobranchia are virtually all marine species, some shelled and some not, and comprise about 25 families and 2000 species of the bubble shells, the seaslugs, as well as the sea hares. The internal organs of the opisthobranchs have undergone detorsion (unwinding of the viscera that were twisted during torsion). * The Pulmonata comprises about 20000 species, includes the majority of land snails and slugs, many freshwater snails, and a small number of marine species. The mantle cavity of the Pulmonata is modified into an air-breathing organ. They are also characterized by detorsion and a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Distance Matrix
In mathematics, computer science and especially graph theory, a distance matrix is a square matrix (two-dimensional array) containing the distances, taken pairwise, between the elements of a set. Depending upon the application involved, the ''distance'' being used to define this matrix may or may not be a metric (mathematics), metric. If there are elements, this matrix will have size . In graph-theoretic applications, the elements are more often referred to as points, nodes or vertices. Non-metric distance matrix In general, a distance matrix is a weighted adjacency matrix of some graph. In a Network (mathematics), network, a directed graph with weights assigned to the arcs, the distance between two nodes of the network can be defined as the minimum of the sums of the weights on the shortest paths joining the two nodes (where the number of steps in the path is bounded). This distance function, while well defined, is not a metric. There need be no restrictions on the weights oth ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
