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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] |
Computational Phylogenetics
Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, Heuristic (computer science), heuristics, and approaches involved in Phylogenetics, phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Maximum likelihood estimation, Maximum likelihood, Maximum parsimony (phylogenetics), parsimony, Bayesian inference in phylogeny, Bayesian, and minimum evolution are typical optimality criteria used to assess how well a phylogenetic tree topology describes the sequence data. Nearest Neighbour Interchange (NNI), Subtree Prune and Regraft (SPR), and Tree Bisection and Reconnection (TBR), known as tree rearrangements, are deterministic algorithms to search for optimal or the best phylogenetic tree. The space and the landscape of searching for the optimal phylogenetic tree is known as phylogeny search space. Maximum Likelihood (al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BAli-Phy
BAli-Phy is a free software program for simultaneously estimating a multiple sequence alignment and its phylogenetic tree. BAli-Phy achieves high accuracy in alignment estimation by using information from the co-estimated phylogeny. BAli-Phy takes alignment uncertainty into account while estimating the phylogeny by averaging over possible alignments. Unlike most phylogeny inference software, input sequences need not be aligned beforehand. This differs from traditional approaches to alignment and phylogeny estimation, which first estimate the alignment without a high-quality tree estimate, and then estimate the tree given the alignment. BAli-Phy produces a Bayesian posterior distribution on both the alignments and the tree. The software shows uncertainty in both the alignment and the tree. BAli-Phy uses Markov chain Monte Carlo methods for estimation. It can take several days to run. Alignment uncertainty Alignment uncertainty stems from two main sources: near-optimal ali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MrBayes
Bayesian inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood model. Bayesian inference was introduced into molecular phylogenetics in the 1990s by three independent groups: Bruce Rannala and Ziheng Yang in Berkeley, Bob Mau in Madison, and Shuying Li in University of Iowa, the last two being PhD students at the time. The approach has become very popular since the release of the MrBayes software in 2001, and is now one of the most popular methods in molecular phylogenetics. Bayesian inference of phylogeny background and bases Bayesian inference refers to a probabilistic method developed by Reverend Thomas Bayes based on Bayes' theorem. Published posthumously in 1763 it was the first expression of inverse probability and the basis of Bayesian inference. Independently, unaware of Bayes' work, Pierre- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Algorithm
In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA). Genetic algorithms are commonly used to generate high-quality solutions to optimization and search problems via biologically inspired operators such as selection, crossover, and mutation. Some examples of GA applications include optimizing decision trees for better performance, solving sudoku puzzles, hyperparameter optimization, and causal inference. Methodology Optimization problems In a genetic algorithm, a population of candidate solutions (called individuals, creatures, organisms, or phenotypes) to an optimization problem is evolved toward better solutions. Each candidate solution has a set of properties (its chromosomes or genotype) which can be mutated and altered; traditionally, solutions are represented in binary as strings of 0s and 1s, but other encod ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wayne Maddison
Wayne Paul Maddison (born 1958) is a Canadian evolutionary biologist, arachnologist, and biological illustrator. He is Canada Research Chair in Biodiversity and a professor at the departments of zoology and botany at the University of British Columbia, and the Director of the Spencer Entomological Collection at the Beaty Biodiversity Museum. Education and career Maddison was born in London, Ontario and his interests in studying spiders started while he was a teenager exploring Lake Ontario. Maddison studied zoology at the University of Toronto, where he obtained his BSc in 1980. He went on to study at Harvard University in the Department of Organismic and Evolutionary Biology, where he obtained his PhD in 1988 under the supervision of Herbert W. Levi. He was a NSERC postdoctoral fellow at the University of California, Berkeley from 1988 to 1990, where he worked with Montgomery Slatkin. Maddison became an assistant professor and later associate professor at the University o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mesquite (software)
Mesquite is a software package primarily designed for phylogenetic analyses. It was developed as a successor to MacClade, when the authors recognized that implementing a modular architecture in MacClade would be infeasible. Mesquite is largely written in Java and uses NEXUS-formatted files as input. Mesquite is available as a compiled executable for Macintosh, Windows, and Unix-like platforms, and the source code is available on GitHub. Rationale The architecture of Mesquite was explicitly designed to exploit the modularity and extensibility of Object-oriented programming. In practice, Mesquite ''modules'' are Java classes, usually concrete sub-classes of abstract class definitions. This modular architecture has afforded the development of additional packages that can be used as plug-ins to Mesquite. Scope Mesquite provides a number of analyses including ancestral state estimation and diversification analysis. Mesquite also contains tools for simulating data such as species ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MEGA, Molecular Evolutionary Genetics Analysis
Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. It includes many sophisticated methods and tools for phylogenomics and phylomedicine. It is licensed as proprietary freeware. The project for developing this software was initiated by the leadership of Masatoshi Nei in his laboratory at the Pennsylvania State University in collaboration with his graduate student Sudhir Kumar and postdoctoral fellow Koichiro Tamura.Kumar, S., K. Tamura, and M. Nei (1993) MEGA: Molecular Evolutionary Genetics Analysis. Ver. 1.0, The Pennsylvania State University, University Park, PA. Nei wrote a monograph (pp. 130) outlining the scope of the software and presenting new statistical methods that were included in MEGA. The entire set of computer programs was written by Kumar and Tamura. The personal computers then lacked the ability to send the monograph and software electronica ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MinHash
In computer science and data mining, MinHash (or the min-wise independent permutations locality sensitive hashing scheme) is a technique for quickly estimating how similar two sets are. The scheme was published by Andrei Broder in a 1997 conference, and initially used in the AltaVista search engine to detect duplicate web pages and eliminate them from search results.. It has also been applied in large-scale clustering problems, such as clustering documents by the similarity of their sets of words.. Jaccard similarity and minimum hash values The Jaccard similarity coefficient is a commonly used indicator of the similarity between two sets. Let be a set and and be subsets of , then the Jaccard index is defined to be the ratio of the number of elements of their intersection and the number of elements of their union: : J(A,B) = . This value is 0 when the two sets are disjoint, 1 when they are equal, and strictly between 0 and 1 otherwise. Two sets are more similar (i.e. have ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
HYPHY (software)
The term hyphy ( ) is an Oakland, California, slang meaning "hyperactive". More specifically, it is an adjective describing the hip-hop music and the culture associated with the Oakland area. The term was first coined by rapper Keak da Sneak. History The hyphy culture emerged in the late 1990s in Oakland before rising to prominence throughout the wider Bay Area in the early 2000s. It is distinguished by gritty, pounding rhythms, and has been compared to crunk music. San Jose producer Traxamillion is largely considered the first producer to create hyphy style music, having produced songs such as Keak Da Sneak's "Super Hyphy", which established the term hyphy. An individual is said to "get hyphy" when they dance in an overstated, fast-paced and ridiculous manner, or if they get overly loud with other people. The phrase ''"to get hyphy"'' is similar to the southern phrase ''"to get crunk"''. Those who consider themselves part of the hyphy movement strive for this behavior. A ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
