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PhyloXML
PhyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data. The structure of phyloXML is described by XML Schema Definition (XSD) language. A shortcoming of current formats for describing phylogenetic trees (such as Nexus and Newick/New Hampshire) is a lack of a standardized means to annotate tree nodes and branches with distinct data fields (which in the case of a basic species tree might be: species names, branch lengths, and possibly multiple support values). Data storage and exchange is even more cumbersome in studies in which trees are the result of a reconciliation of some kind: * gene-function studies (requires annotation of nodes with taxonomic information as well as gene names, and possibly gene-duplication data) * evolution of host-parasite interactions (requires annotation of tree nodes with taxonomic information for both host and parasite) * phylogeographic studies (requires annotation of tree nodes wit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics (also phylogeny inference) focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape. Phylogenetic trees may be rooted or unrooted. In a ''rooted'' p ... [...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] |
Newick Format
In mathematics and phylogenetics, Newick tree format (or Newick notation or New Hampshire tree format) is a way of representing graph-theoretical trees with edge lengths using parentheses and commas. It was adopted by James Archie, William H. E. Day, Joseph Felsenstein, Wayne Maddison, Christopher Meacham, F. James Rohlf, and David Swofford, at two meetings in 1986, the second of which was at Newick's restaurant in Dover, New Hampshire, US. The adopted format is a generalization of the format developed by Meacham in 1984 for the first tree-drawing programs in Felsenstein's PHYLIP package. Examples The following tree: could be represented in Newick format in several ways ((,)); ''no nodes are named'' (A,B,(C,D)); ''leaf nodes are named'' (A,B,(C,D)E)F; ''all nodes are named'' (:0.1,:0.2,(:0.3,:0.4):0.5); ''all but root node have a distance to parent'' (:0.1,:0.2,(:0.3,:0.4):0.5): ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NHX Format
Isthmus Nahuatl (Isthmus Nahuat; native name: ''melatájto̱l'') is a Nahuatl dialect cluster spoken by about 30,000 people in Veracruz, Mexico. According to ''Ethnologue'' 16, the Cosoleacaque dialect is 84% intelligible with Pajapan, and 83% intelligible with Mecayapan. Communities It is spoken in the following Veracruzan communities: * Municipality of Cosoleacaque (settlements of Arroyo el Limón, Bajo Grande, Barrancas (Buenos Aires), Cajiapan, Calzadas (Kilómetro Catorce), Canticas, Cascajal II, Cerro Blanco, Coacotla, Cocal, Colonia Luis Donaldo Colosio, Cosoleacaque, Desviación a San Antonio, Ejido la Bomba, Ejido la Colmena, El Rincón de la Colmena (Sección Carrizal), El Arenal, El Bejarito, El Cascajal, El Colorado, El Conejo, El Coyote, El Gavilán, El Kilómetro Diecisiete, El Limón, El Manguito, El Nacaste, El Nanchital, El Naranjito, El Naranjo, El Oasis, El Palmar, El Piñal, El Potrerillo, El Soriano, El Zapote, Entrada a Zapotal, Estero del Pantano, Fernand ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Archaeopteryx (evolutionary Tree Visualization And Analysis)
Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees. This type of program can be used for a variety of analyses of molecular data sets, but is particularly designed for phylogenomics Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields .... Besides tree description formats with limited expressiveness (such as Newick/New Hamphshire, Nexus), it also implements the phyloXML format. Archaeopteryx is the successor to Java program ''A Tree Viewer'' (ATV). References External linksphyloXML * ttp://www.phylosoft.org/archaeopteryx/ Archaeopteryx {{genomics-footer Phylogenetics software ... [...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), unweighted pair group method with arithmetic mean (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 Geneti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
