phylo-node: A molecular phylogenetic toolkit using Node.js.
<h4>Background</h4>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...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0175480 |
| _version_ | 1819017173897576448 |
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| author | Damien M O'Halloran |
| author_facet | Damien M O'Halloran |
| author_sort | Damien M O'Halloran |
| collection | DOAJ |
| description | <h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusions</h4>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. |
| first_indexed | 2024-12-21T02:59:19Z |
| format | Article |
| id | doaj.art-eaec53c1292f4a34894cf5282b7d8599 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T02:59:19Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-eaec53c1292f4a34894cf5282b7d85992022-12-21T19:18:14ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01124e017548010.1371/journal.pone.0175480phylo-node: A molecular phylogenetic toolkit using Node.js.Damien M O'Halloran<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusions</h4>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.https://doi.org/10.1371/journal.pone.0175480 |
| spellingShingle | Damien M O'Halloran phylo-node: A molecular phylogenetic toolkit using Node.js. PLoS ONE |
| title | phylo-node: A molecular phylogenetic toolkit using Node.js. |
| title_full | phylo-node: A molecular phylogenetic toolkit using Node.js. |
| title_fullStr | phylo-node: A molecular phylogenetic toolkit using Node.js. |
| title_full_unstemmed | phylo-node: A molecular phylogenetic toolkit using Node.js. |
| title_short | phylo-node: A molecular phylogenetic toolkit using Node.js. |
| title_sort | phylo node a molecular phylogenetic toolkit using node js |
| url | https://doi.org/10.1371/journal.pone.0175480 |
| work_keys_str_mv | AT damienmohalloran phylonodeamolecularphylogenetictoolkitusingnodejs |