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SplitsTree
SplitsTree is a popular freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, splits graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees. SplitsTree implements published methods such as split decomposition, neighbor-net, consensus networks, super networks methods or methods for computing hybridization or simple recombination networks. It uses the NEXUS file format. The splits graph is defined using a special data block (SPLITS block). See also *Phylogenetic tree viewers *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 analyse ... * MEGAN References External links SplitsTree homepage(New Website for informations about SplitsTree)for the latest version (4.15) and manual (June 201 ... [...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 been ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nexus File
The extensible NEXUS file format is widely used in bioinformatics. It stores information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc. Several popular phylogenetic programs such as PAUP*,PAUP* — Phylogenetic Analysis Using Parsimony *and other methods ,MrBayes /ref> Mesquite,Mesquite: A modular system for ev ... [...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] |
Split (phylogenetics)
A split in phylogenetics is a bipartition of a set of taxon, taxa, and the smallest unit of information in unrooted phylogenetic trees: 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. See also *SplitsTree SplitsTree is a popular freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, splits graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees. SplitsTree impleme ..., a program for inferring phylogenetic (split) networks. References {{reflist Phylogenetics Trees (data structures) ... [...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 (mathematics), hierarchy, and are represented using a type of phylogenetic network called a Split graph, 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 (programming language), R/Phangorn packages. Examples of the application of Neighbor-net can be found in virology, horticulture, dinosaur genetics, Quantitative comparative linguistics, comparative linguistics, and archaeology. References Computational phylogenetics Genetics software Molecular biology {{bioinformatics-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetics Software
This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenies include neighbor-joining, maximum parsimony (also simply referred to as parsimony), UPGMA, Bayesian phylogenetic inference, maximum likelihood and distance matrix methods. List See also *List of phylogenetic tree visualization software References External links *Complete list oInstitut Pasteurphylogeny webserversExPASyList of phylogenetics programs *A verof phylogenetic tools (reconstruction, visualization, ''etc.'') *Anothelist of evolutionary genetics software*A list ophylogenetic softwareprovided by the Zoological Research Museum A. Koenig *MicrobeTrace available at https://github.com/CDCgov/MicrobeTrace/wiki {{DEFAULTSORT:List Of Phylogenetics Software Genetics databases Phylo Phylogenetics In biology, phylo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Tree Viewers
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 |
University Of Tübingen
The University of Tübingen, officially the Eberhard Karl University of Tübingen (german: Eberhard Karls Universität Tübingen; la, Universitas Eberhardina Carolina), is a public research university located in the city of Tübingen, Baden-Württemberg, Germany. The University of Tübingen is one of eleven German Excellence Universities. The University of Tübingen is especially known as a centre for the study of plant biology, medicine, law, archeology, ancient cultures, philosophy, theology, and religious studies as well as more recently as center of excellence for artificial intelligence. The university's noted alumni include presidents, EU Commissioners, and judges of the Federal Constitutional Court. The university is associated with eleven Nobel laureates, especially in the fields of medicine and chemistry. History The University of Tübingen was founded in 1477 by Count Eberhard V (Eberhard im Bart, 1445–1496), later the first Duke of Württemberg, a civic and ... [...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. Megan is also frequently spelled Meagan, Meaghan, or Meghan outside of Wales and the rest of the United Kingdom due to spelling influence from Irish-language names. People * Meagan Best (born 2002), Barbadian squash player * Megan Bonnell, Canadian musician * Meghan Boody (born 1964), American surrealist photographer * Megan Boone (born 1983), American actress * Megan Cunningham (born 1995), Scottish footballer * Megan Danso (born 1990), Cana ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heterobranchia Tree
Heterobranchia, the ''heterobranchs'' (meaning "different-gilled snails"), is a taxonomic clade of snails and slugs, which includes marine, aquatic and terrestrial gastropod mollusks. Heterobranchia is one of the main clades of gastropods. Currently Heterobranchia comprises three informal groups: the lower heterobranchs, the opisthobranchs and the pulmonates.Bouchet P. & Rocroi J.-P. (Ed.); Frýda J., Hausdorf B., Ponder W., Valdes A. & Warén A. 2005. ''Classification and nomenclator of gastropod families''. Malacologia: International Journal of Malacology, 47(1-2). ConchBooks: Hackenheim, Germany. . . 397 pp. http://www.vliz.be/Vmdcdata/imis2/ref.php?refid=78278 Diversity The three subdivisions of this large clade are quite diverse: * The Lower Heterobranchia includes shelled marine and freshwater species. * Opisthobranchia are almost all marine species, some shelled and some not. The internal organs of the opisthobranchs have undergone detorsion (unwinding of the vis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...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 se ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
