phylo-node: A Molecular Phylogenetic Toolkit using Node.js

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.\n\nResults: 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 go from sequence retrieval to phylogeny reconstruction. Phylo-Node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for sequence retrieval, 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.\n\nConclusions: 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