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Phylogenetic Assignment Of Named Global Outbreak Lineages
The Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) is a software tool developed by Dr. Áine O'Toole and members of the Andrew Rambaut laboratory, with an associated web application developed by the Centre for Genomic Pathogen Surveillance in South Cambridgeshire. Its purpose is to implement a dynamic nomenclature (known as the Pango nomenclature) to classify Lineage (genetic), genetic lineages for SARS-CoV-2, the virus that causes COVID-19. A user with a full genome sequence of a sample of SARS-CoV-2 can use the tool to submit that sequence, which is then compared with other genome sequences, and assigned the most likely lineage (Pango lineage). Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage. Additionally, it interfaces with Microreact, to show a time sequence of the location of reports of sequenced samples of the same lineage. This latter feature draws on publicly available ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python (programming Language)
Python is a high-level programming language, high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is type system#DYNAMIC, dynamically type-checked and garbage collection (computer science), garbage-collected. It supports multiple programming paradigms, including structured programming, structured (particularly procedural programming, procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC (programming language), ABC programming language, and he first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000. Python 3.0, released in 2008, was a major revision not completely backward-compatible with earlier versions. Python 2.7.18, released in 2020, was the last release of ... [...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] |
Genome Databases
A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics. The genomes of many organisms have been sequenced and various regions have been annotated. The first genome to be sequenced was that of the virus φX174 in 1977; the first genome sequence of a prokaryote (''Haemophilus influenzae'') was published in 1995; the yeast (''Saccharomyces cerevisiae'') genome was the first eukaryotic genome to be sequenced in 1996. The Human Genome Project was started in October 1990, and the first draft sequence ... [...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] |
INSDC
The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. It involves the following computerized databases: NIG's DNA Data Bank of Japan (Japan), NCBI's GenBank ( USA) and the EMBL- EBI's European Nucleotide Archive ( EMBL). New and updated data on nucleotide sequences contributed by research teams to each of the three databases are synchronized on a daily basis through continuous interaction between the staff at each the collaborating organizations. All of the data in INSDC is available for free and unrestricted access, for any purpose, with no restrictions on analysis, redistribution, or re-publication of the data. This policy has been a foundational principle of the INSDC since its inception. Since the 1990s, most of the world's major scientific journals have required that sequence data be deposited in an INSDC database as a pre-condition for publication. The DDBJ/ EMBL ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nextstrain
Nextstrain is a collaboration between researchers in Seattle, United States and Basel, Switzerland which provides a collection of open-source tools for visualising the genetics behind the spread of viral outbreaks. Its aim is to support public health measures and surveillance by facilitating understanding of the spread and evolution of pathogens. The Nextstrain platform was begun in 2015. Code developed by Nextstrain is made publicly available, via, for example GitHub, github.com and its data is available and viewable in accessible form via the pages at the website. Applications According to their website, the Nextstrain team maintains an up-to-date genomic analysis of each of the following pathogens: * Avian influenza * Dengue * Enterovirus D68 * Measles * Monkeypox virus * Mumps * SARS-CoV-2 * Seasonal influenza * Tuberculosis * West Nile virus * Western African Ebola virus epidemic, West African Ebola 2013-16 * Zika Covid-19 pandemic Nextstrain and its results have been wide ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Variants Of SARS-CoV-2
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are viruses that, while similar to the original, have genetic changes that are of enough significance to lead virologists to label them separately. SARS-CoV-2 is the virus that causes coronavirus disease 2019 (COVID-19). Some have been stated, to be of particular importance due to their potential for increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them. These variants contribute to the continuation of the COVID-19 pandemic. , the variants of interest as specified by the World Health Organization are JN.1, and the variants under monitoring are KP.3, KP.3.1.1, JN.1.18, LB.1, LP.8.1, NB.1.8.1 and XEC. Overview The origin of SARS-CoV-2 has not been identified. However, the emergence of SARS-CoV-2 may have resulted from recombination events between a bat SARS-like coronavirus and a pangolin coronavirus through cross-species transmission. The earliest availa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Colloquial Names Of COVID-19 Variants
During the early days of the COVID-19 pandemic, the disease and virus were sometimes called "coronavirus", "novel coronavirus", "Wuhan coronavirus", or "Wuhan pneumonia". In January 2020, the World Health Organization (WHO) tentatively named it "2019-nCoV", short for "2019 Novel Coronavirus", or "2019 Novel Coronavirus Acute Respiratory Disease". This naming was based on the organization's 2015 guidelines for naming novel viruses and diseases, avoiding the use of geographic locations (such as Wuhan), in part to prevent social stigma. A similar structure has also been used by the AP when referring to virus variants, for example, referring to it as the "Delta variant" rather than the "South African variant". On 11 February 2020, the WHO named the disease COVID-19 (short for coronavirus disease 2019). That same day, the International Committee on Taxonomy of Viruses (ICTV) formally announced it had named the causative virus as SARS-CoV-2 (severe acute respiratory syndrome coronavi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Conda (package Manager)
Conda is an open-source, cross-platform, language-agnostic package manager and environment management system. It was originally developed to solve package management challenges faced by Python data scientists, and today is a popular package manager for Python and R. At first, Anaconda Python distribution was developed by Anaconda Inc.; later, it was spun out as a separate package, released under the BSD license. The Conda package and environment manager is included in all versions of Anaconda, Miniconda, and Anaconda Repository. Conda is a NumFOCUS affiliated project. Features As a package manager, Conda allows users to install different versions of binary software packages and their required software dependencies appropriate for their computing platform from a software repository. Conda checks everything that has been installed, any version limitations that the user specifies (for example, the user wants a specific package to be at least version 2.1.3), and determin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Command Line
A command-line interface (CLI) is a means of interacting with software via command (computing), commands each formatted as a line of text. Command-line interfaces emerged in the mid-1960s, on computer terminals, as an interactive and more user-friendly alternative to the non-interactive mode available with punched cards. For a long time, a CLI was the most common interface for software, but today a graphical user interface (GUI) is more common. Nonetheless, many programs such as operating system and software development utility software, utilities still provide CLI. A CLI enables automation, automating computer program, programs since commands can be stored in a scripting language, script computer file, file that can be used repeatedly. A script allows its contained commands to be executed as group; as a program; as a command. A CLI is made possible by command-line interpreters or command-line processors, which are programs that execute input commands. Alternatives to a CLI ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scikit-learn
scikit-learn (formerly scikits.learn and also known as sklearn) is a free and open-source machine learning library for the Python programming language. It features various classification, regression and clustering algorithms including support-vector machines, random forests, gradient boosting, ''k''-means and DBSCAN, and is designed to interoperate with the Python numerical and scientific libraries NumPy and SciPy. Scikit-learn is a NumFOCUS fiscally sponsored project. Overview The scikit-learn project started as scikits.learn, a Google Summer of Code project by French data scientist David Cournapeau. The name of the project derives from its role as a "scientific toolkit for machine learning", originally developed and distributed as a third-party extension to SciPy. The original codebase was later rewritten by other developers. In 2010, contributors Fabian Pedregosa, Gaël Varoquaux, Alexandre Gramfort and Vincent Michel, from the French Institute for Research in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GitHub
GitHub () is a Proprietary software, proprietary developer platform that allows developers to create, store, manage, and share their code. It uses Git to provide distributed version control and GitHub itself provides access control, bug tracking system, bug tracking, software feature requests, task management, continuous integration, and wikis for every project. Headquartered in California, GitHub, Inc. has been a subsidiary of Microsoft since 2018. It is commonly used to host open source software development projects. GitHub reported having over 100 million developers and more than 420 million Repository (version control), repositories, including at least 28 million public repositories. It is the world's largest source code host Over five billion developer contributions were made to more than 500 million open source projects in 2024. About Founding The development of the GitHub platform began on October 19, 2005. The site was launched in April 2008 by Tom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
