phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics
Background While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, ex...
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| Vydané v: | BMC bioinformatics Ročník 19; číslo 1; s. 276 - 5 |
|---|---|
| Hlavní autori: | , , |
| Médium: | Journal Article |
| Jazyk: | English |
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London
BioMed Central
25.07.2018
BioMed Central Ltd Springer Nature B.V BMC |
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| ISSN: | 1471-2105, 1471-2105 |
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| Abstract | Background
While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application.
Results
phylotree.js
is a library that extends the popular data visualization framework
d3.js
, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees.
phylotree.js
implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram.
Conclusions
phylotree.js
is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license. |
|---|---|
| AbstractList | While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application.BACKGROUNDWhile several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application.phylotree.js is a library that extends the popular data visualization framework d3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees. phylotree.js implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram.RESULTSphylotree.js is a library that extends the popular data visualization framework d3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees. phylotree.js implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram.phylotree.js is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license.CONCLUSIONSphylotree.js is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license. Background While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application. Results phylotree.js is a library that extends the popular data visualization framework d3.js , and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees. phylotree.js implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram. Conclusions phylotree.js is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license. While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application. phylotree.js is a library that extends the popular data visualization framework d3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees. phylotree.js implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram. phylotree.js is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license. BackgroundWhile several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application.Resultsphylotree.js is a library that extends the popular data visualization framework d3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees. phylotree.js implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram.Conclusionsphylotree.js is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license. Background While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application. Results phylotree.js is a library that extends the popular data visualization framework d3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees. phylotree.js implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram. Conclusions phylotree.js is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license. Keywords: Phylogenetics, JavaScript, Data visualization, D3 While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application. phylotree.js is a library that extends the popular data visualization framework d3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees. phylotree.js implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram. phylotree.js is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license. Abstract Background While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application. Results phylotree.js is a library that extends the popular data visualization framework d3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees. phylotree.js implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram. Conclusions phylotree.js is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license. |
| ArticleNumber | 276 |
| Audience | Academic |
| Author | Shank, Stephen D. Weaver, Steven Kosakovsky Pond, Sergei L. |
| Author_xml | – sequence: 1 givenname: Stephen D. orcidid: 0000-0003-0734-9953 surname: Shank fullname: Shank, Stephen D. email: sshank@temple.edu organization: Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University – sequence: 2 givenname: Steven surname: Weaver fullname: Weaver, Steven organization: Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University – sequence: 3 givenname: Sergei L. surname: Kosakovsky Pond fullname: Kosakovsky Pond, Sergei L. organization: Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30045713$$D View this record in MEDLINE/PubMed |
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| References | M Bostock (2283_CR7) 2011; 17 AG Meyer (2283_CR14) 2015; 11 S Weaver (2283_CR12) 2018; 35 O Robinson (2283_CR4) 2016; 33 PSL Kosakovsky (2283_CR15) 2005; 22 RA Vos (2283_CR11) 2012; 61 Ł Kreft (2283_CR3) 2017; 33 2283_CR16 SA Smits (2283_CR5) 2010; 5 TG Vaughan (2283_CR2) 2017; 33 MV Han (2283_CR10) 2009; 10 JO Wertheim (2283_CR13) 2014; 32 C Darwin (2283_CR1) 1859 2283_CR6 SLK Pond (2283_CR8) 2005 AJ Drummond (2283_CR9) 2007; 7 B Venkatachalam (2283_CR17) 2010; 7 |
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While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a... While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of... Background While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a... BackgroundWhile several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a... Abstract Background While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed... |
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| Title | phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics |
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