phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics

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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.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2283-2) contains supplementary material, which is available to authorized users.

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Most cited references 6

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D³: Data-Driven Documents.

Michael Bostock, Vadim Ogievetsky, Jeffrey Heer (2011)

Data-Driven Documents (D3) is a novel representation-transparent approach to visualization for the web. Rather than hide the underlying scenegraph within a toolkit-specific abstraction, D3 enables direct inspection and manipulation of a native representation: the standard document object model (DOM). With D3, designers selectively bind input data to arbitrary document elements, applying dynamic transforms to both generate and modify content. We show how representational transparency improves expressiveness and better integrates with developer tools than prior approaches, while offering comparable notational efficiency and retaining powerful declarative components. Immediate evaluation of operators further simplifies debugging and allows iterative development. Additionally, we demonstrate how D3 transforms naturally enable animation and interaction with dramatic performance improvements over intermediate representations. © 2010 IEEE

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NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

Rutger A Vos, James Balhoff, Jason Caravas … (2012)

In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input–output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.

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IcyTree: rapid browser-based visualization for phylogenetic trees and networks

Timothy Vaughan (2017)

Abstract Summary: IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. Availability and Implementation: IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree. Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. Contact: tgvaughan@gmail.com

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Author and article information

Contributors

Stephen D. Shank:

ORCID: http://orcid.org/0000-0003-0734-9953

sshank@temple.edu

Steven Weaver: sweaver@temple.edu

Sergei L. Kosakovsky Pond: spond@temple.edu

Journal

Journal ID (nlm-ta): BMC Bioinformatics

Journal ID (iso-abbrev): BMC Bioinformatics

Title: BMC Bioinformatics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2105

Publication date (Electronic): 25 July 2018

Publication date PMC-release: 25 July 2018

Publication date Collection: 2018

Volume: 19

Electronic Location Identifier: 276

Affiliations

ISNI 0000 0001 2248 3398, GRID grid.264727.2, Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, ; Philadelphia, 19122 USA

Author information

Stephen D. Shank http://orcid.org/0000-0003-0734-9953

Article

Publisher ID: 2283

DOI: 10.1186/s12859-018-2283-2

PMC ID: 6060545

PubMed ID: 30045713

SO-VID: 979dac60-1cc7-4c6d-a011-1d4bc2825c2b

License:

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 26 January 2018

Date accepted : 11 July 2018

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;

Award ID: GM093939

Award Recipient : Sergei L. Kosakovsky Pond

Funded by: FundRef http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;

Award ID: AI134384

Award Recipient : Sergei L. Kosakovsky Pond

Funded by: FundRef http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;

Award ID: GM110749

Award Recipient : Sergei L. Kosakovsky Pond

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ScienceOpen disciplines: Bioinformatics & Computational biology

Keywords: phylogenetics,javascript,data visualization,d3

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ScienceOpen disciplines: Bioinformatics & Computational biology

Keywords: phylogenetics, javascript, data visualization, d3

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phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics

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Abstract

Background

Results

Conclusions

Electronic supplementary material

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REPO4EU WP2 Tools

Most cited references 6

D³: Data-Driven Documents.

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

IcyTree: rapid browser-based visualization for phylogenetic trees and networks

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Cited by 24

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