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phylo-node: A molecular phylogenetic toolkit using Node.js

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  • Damien M O’Halloran

Abstract

Background: Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. Results: To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. Conclusions: phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

Suggested Citation

  • Damien M O’Halloran, 2017. "phylo-node: A molecular phylogenetic toolkit using Node.js," PLOS ONE, Public Library of Science, vol. 12(4), pages 1-8, April.
    • Handle: RePEc:plo:pone00:0175480
    DOI: 10.1371/journal.pone.0175480
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    1. Julie D Thompson & Benjamin Linard & Odile Lecompte & Olivier Poch, 2011. "A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-14, March.
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