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Robert C. Edgar
MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain. The method was published by Robert C. Edgar in two papers in 2004. The first paper, published in ''Nucleic Acids Research'', introduced the sequence alignment algorithm. The second paper, published in ''BMC Bioinformatics'', presented more technical details. Algorithm The MUSCLE algorithm proceeds in three stages: the ''draft progressive'', ''improved progressive'', and ''refinement'' stage. Stage 1: Draft Progressive In this first stage, the algorithm produces a multiple alignment, emphasizing speed over accuracy. This step begins by computing the k-mer distance for every pair of input sequences to create a distance matrix. UPGMA clusters the distance matrix to produce a binary tree. From this tree a progressive alignment is constructed, beginning with the creation of profiles for each leaf of the tree ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linux
Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which includes the kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name "GNU/Linux" to emphasize the importance of GNU software, causing some controversy. Popular Linux distributions include Debian, Fedora Linux, and Ubuntu, the latter of which itself consists of many different distributions and modifications, including Lubuntu and Xubuntu. Commercial distributions include Red Hat Enterprise Linux and SUSE Linux Enterprise. Desktop Linux distributions include a windowing system such as X11 or Wayland, and a desktop environment such as GNOME or KDE Plasma. Distributions intended for ser ... [...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. 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, 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. This distance function, while well defined, is not a metric. There need be no restrictions on the weights other than the need to be able to combine and compare them, so negative weights are used in some appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Plug-in (computing)
In computing, a plug-in (or plugin, add-in, addin, add-on, or addon) is a software component that adds a specific feature to an existing computer program. When a program supports plug-ins, it enables customization. A theme or skin is a preset package containing additional or changed graphical appearance details, achieved by the use of a graphical user interface (GUI) that can be applied to specific software and websites to suit the purpose, topic, or tastes of different users to customize the look and feel of a piece of computer software or an operating system front-end GUI (and window managers). Purpose and examples Applications may support plug-ins to: * enable third-party developers to extend an application * support easily adding new features * reduce the size of an application by not loading unused features * separate source code from an application because of incompatible software licenses. Types of applications and why they use plug-ins: * Digital audio workstation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UGENE
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2. UGENE helps biologists to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. The data can be stored both locally (on a personal computer) and on a shared storage (e.g., a lab database). UGENE integrates dozens of well-known biological tools, algorithms, and original tools in the context of genomics, evolutionary biology, virology, and other branches of life science. UGENE provides a graphical user interface (GUI) for the pre-built tools so biologists with no computer programming skills can access those tools more easily. Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data readers, blocks ... [...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 electronicall ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequencher
Gene Codes Corporation is a privately owned international firm based in Ann Arbor, Michigan, which specializes in bioinformatics software for genetic sequence analysis In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence alig .... Its flagship software product, Sequencher, is a sequencing software used throughout the world. Its targeted use is by researchers at academic and government labs as well as biotechnology and pharmaceutical companies for DNA sequence assembly. History Gene Codes Corporation was founded in 1988 in Ann Arbor, Michigan. In 1991, the DNA sequence assembly and analysis software, Sequencher, was released. By 1997, nearly every major pharmaceutical company and commercial genomics company in the world was standardized on Sequencher, as well as the majority of labs at majo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MacVector
MacVector is a commercial sequence analysis application for Apple Macintosh computers running Mac OS X. It is intended to be used by Molecular biology, molecular biologists to help analyze, design, research and document their experiments in the laboratory. MacVector 18.1 is a Universal binary, Universal Binary capable of running on Intel and Apple Silicon Macs. Features MacVector is a collection of sequence analysis algorithms linked to various sequence editors, including a single sequence editor, a multiple sequence alignment editor and a contig editor. MacVector tries to use a minimum of windows and steps to access all the functionality. Functions include: * Sequence alignment (ClustalW, MUSCLE (alignment software), Muscle and T-COFFEE, T-Coffee) and editing. * Subsequence search and open reading frames (ORFs) analysis. * Phylogenetic tree construction UPGMA, Neighbour joining with bootstrapping and consensus trees * Online Database searching - Search public databases at the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNASTAR
DNASTAR is a global bioinformatics software company incorporated in 1984 that is headquartered in Madison, Wisconsin. DNASTAR develops and sells software for sequence analysis in the fields of genomics, molecular biology, and structural biology. Software DNASTAR software (Lasergene) first gained popularity in the 1980s and 1990s for its sequence assembly and analysis capabilities of Sanger sequencing data. Lasergene 17.3.3 was released in June 2022. DNASTAR software is available for desktop computers running Mac OS X, Windows, and Linux as well as for use on Amazon Web Services. In 2007, DNASTAR expanded their offerings to include software for next-generation sequencing and structural biology. DNASTAR's next-gen software supports data from Illumina, Ion Torrent, and Pacific Biosciences and allows the user to assemble, align, analyze and visualize genomic data. Lasergene's use in next-generation sequence assembly and analysis was contributed as a chapter, written by company sci ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Clustal
Clustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its algorithm are also detailed in their respective categories. Available operating systems listed in the sidebar are a combination of the software availability and may not be supported for every current version of the Clustal tools. Clustal Omega has the widest variety of operating systems out of all the Clustal tools. History There have been many variations of the Clustal software, all of which are listed below: * Clustal: The original software for multiple sequence alignments, created by Des Higgins in 1988, was based on deriving phylogenetic trees from pairwise sequences of amino acids or nucleotides. * ClustalV: The second generation of the Clustal software was released in 1992 and was a rewrite of the original Clustal package. It intr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Space Complexity
The space complexity of an algorithm or a computer program is the amount of memory space required to solve an instance of the computational problem as a function of characteristics of the input. It is the memory required by an algorithm until it executes completely. Similar to time complexity, space complexity is often expressed asymptotically in big O notation, such as O(n), O(n\log n), O(n^\alpha), O(2^n), etc., where is a characteristic of the input influencing space complexity. Space complexity classes Analogously to time complexity classes DTIME(f(n)) and NTIME(f(n)), the complexity classes DSPACE(f(n)) and NSPACE(f(n)) are the sets of languages that are decidable by deterministic (respectively, non-deterministic) Turing machines that use O(f(n)) space. The complexity classes PSPACE and NPSPACE allow f to be any polynomial, analogously to P and NP. That is, :\mathsf = \bigcup_ \mathsf(n^c) and :\mathsf = \bigcup_ \mathsf(n^c) Relationships between classes The space ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Time Complexity
In computer science, the time complexity is the computational complexity that describes the amount of computer time it takes to run an algorithm. Time complexity is commonly estimated by counting the number of elementary operations performed by the algorithm, supposing that each elementary operation takes a fixed amount of time to perform. Thus, the amount of time taken and the number of elementary operations performed by the algorithm are taken to be related by a constant factor. Since an algorithm's running time may vary among different inputs of the same size, one commonly considers the worst-case time complexity, which is the maximum amount of time required for inputs of a given size. Less common, and usually specified explicitly, is the average-case complexity, which is the average of the time taken on inputs of a given size (this makes sense because there are only a finite number of possible inputs of a given size). In both cases, the time complexity is generally expresse ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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