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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 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 genomes obtaine ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python (programming Language)
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly 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 and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ranks as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Epidemiological Surveillance
Public health surveillance (also epidemiological surveillance, clinical surveillance or syndromic surveillance) is, according to the World Health Organization (WHO), "the continuous, systematic collection, analysis and interpretation of health-related data needed for the planning, implementation, and evaluation of public health practice."Public health surveillance (accessed January 14, 2016). Public health surveillance may be used to track emerging health-related issues at an early stage and find active solutions in a timely manner. Surveillance systems are generally called upon to provide information regarding when and where heal ... [...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] |
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.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 * Mumps * SARS-CoV-2 * Seasonal influenza * Tuberculosis * West Nile virus * West African Ebola 2013-16 * Zika * Monkeypox virus Covid-19 pandemic Nextstrain and its results have been widely quoted during the COVID-19 pandemic. Awar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Variants Of SARS-CoV-2
There are many variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19). Some are believed, or 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. only the Omicron variant is designated as a circulating variant of concern by the World Health Organization. Overview 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 available SARS-CoV-2 viral genomes were collected from patients in December 2019, and Chinese researchers compared these early genomes with bat and pangolin coronavirus strains to estimate the ancestral human coronavirus type; the identified ancestral genome type ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Conda (package Manager)
Conda is an Open-source software, open-source, cross-platform, language-agnostic package manager and environment management system. It was originally developed to solve difficult package management challenges faced by Python (programming language), Python data science, data scientists, and today is a popular package manager for Python and R (programming language), R. At first part of Anaconda (Python distribution), Anaconda Python distribution developed by Anaconda Inc., it ended up being useful on its own and for things other than Python, so it was spun out as a separate package, released under the BSD licenses, BSD license. The Conda package and environment manager is included in all versions of Anaconda (Python distribution), Anaconda, Miniconda, and Anaconda Repository. Conda is a NumFOCUS affiliated project. Features Conda allows users to easily install different versions of binary file, binary software packages and any required libraries appropriate for their computing ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Command Line
A command-line interpreter or command-line processor uses a command-line interface (CLI) to receive commands from a user in the form of lines of text. This provides a means of setting parameters for the environment, invoking executables and providing information to them as to what actions they are to perform. In some cases the invocation is conditional based on conditions established by the user or previous executables. Such access was first provided by computer terminals starting in the mid-1960s. This provided an interactive environment not available with punched cards or other input methods. Today, many users rely upon graphical user interfaces and menu-driven interactions. However, some programming and maintenance tasks may not have a graphical user interface and use a command line. Alternatives to the command-line interface include text-based user interface menus (for example, IBM AIX SMIT), keyboard shortcuts, and various desktop metaphors centered on the pointer (usual ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scikit-learn
scikit-learn (formerly scikits.learn and also known as sklearn) is a free software 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 stems from the notion that it is a "SciKit" (SciPy Toolkit), a separately developed and distributed 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 Computer Science and Automation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GitHub
GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the distributed version control of Git plus access control, bug tracking, software feature requests, task management, continuous integration, and wikis for every project. Headquartered in California, it has been a subsidiary of Microsoft since 2018. It is commonly used to host open source software development projects. As of June 2022, GitHub reported having over 83 million developers and more than 200 million repositories, including at least 28 million public repositories. It is the largest source code host . History GitHub.com Development of the GitHub.com platform began on October 19, 2007. The site was launched in April 2008 by Tom Preston-Werner, Chris Wanstrath, P. J. Hyett and Scott Chacon after it had been made available for a few months prior as a beta release. GitHub has an annual keynote called GitHub Universe. Organizational ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) 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. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. ''Unrooted'' trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
COVID-19 Pandemic
The COVID-19 pandemic, also known as the coronavirus pandemic, is an ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The novel virus was first identified in an outbreak in the Chinese city of Wuhan in December 2019. Attempts to contain it there failed, allowing the virus to spread to other areas of Asia and later worldwide. The World Health Organization (WHO) declared the outbreak a public health emergency of international concern on 30 January 2020, and a pandemic on 11 March 2020. As of , the pandemic had caused more than cases and confirmed deaths, making it one of the deadliest in history. COVID-19 symptoms range from undetectable to deadly, but most commonly include fever, dry cough, and fatigue. Severe illness is more likely in elderly patients and those with certain underlying medical conditions. COVID-19 transmits when people breathe in air contaminated by droplets and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pangolin
Pangolins, sometimes known as scaly anteaters, are mammals of the order Pholidota (, from Ancient Greek ϕολιδωτός – "clad in scales"). The one extant family, the Manidae, has three genera: '' Manis'', '' Phataginus'', and '' Smutsia''. ''Manis'' comprises the four species found in Asia, while ''Phataginus'' and ''Smutsia'' include two species each, all found in sub-Saharan Africa. These species range in size from . A number of extinct pangolin species are also known. Pangolins have large, protective keratin scales, similar in material to fingernails and toenails, covering their skin; they are the only known mammals with this feature. They live in hollow trees or burrows, depending on the species. Pangolins are nocturnal, and their diet consists of mainly ants and termites, which they capture using their long tongues. They tend to be solitary animals, meeting only to mate and produce a litter of one to three offspring, which they raise for about two years. Pangol ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
