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: Shank, Stephen D., Weaver, Steven, Kosakovsky Pond, Sergei L.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 25.07.2018
BioMed Central Ltd
Springer Nature B.V
BMC
Predmet:
Algorithms
Applications programs
Bioinformatics
Biology
Biomedical and Life Sciences
Comparative genomics
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer applications
Data processing
Data visualization
Genomics
Hypothesis testing
Interoperability
Java
JavaScript
JavaScript (Programming language)
Life Sciences
Metadata
Microarrays
Middleware
Phylogenetics
Phylogeny
Scientific visualization
Software
Visualization
Phylogenetics
Data visualization
JavaScript
D3
ISSN:1471-2105, 1471-2105
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Shrnutí: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.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-018-2283-2