{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T06:07:39Z","timestamp":1788934059775,"version":"build-2803163510"},"reference-count":32,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>\n                    We present\n                    <jats:monospace>Datamonkey 3<\/jats:monospace>\n                    , a browser-native implementation of the\n                    <jats:monospace>Datamonkey<\/jats:monospace>\n                    web platform for molecular evolutionary analysis. By utilizing\n                    <jats:monospace>WebAssembly<\/jats:monospace>\n                    to execute the\n                    <jats:monospace>HyPhy<\/jats:monospace>\n                    analysis engine on the client side,\n                    <jats:monospace>Datamonkey 3<\/jats:monospace>\n                    removes the dependency on remote computational clusters for standard analyses. This architecture ensures data sovereignty by processing sequences locally and enables an interactive workflow with immediate feedback. The platform provides a comprehensive suite of statistical methods for detecting natural selection and recombination, supported by a data curation system that identifies and corrects common formatting errors. Additionally,\n                    <jats:monospace>Datamonkey 3<\/jats:monospace>\n                    incorporates data-driven runtime estimation and interactive results visualization. By shifting the computational burden to the client,\n                    <jats:monospace>Datamonkey 3<\/jats:monospace>\n                    establishes a sustainable, privacy-preserving infrastructure model that scales with the user base, demonstrating the viability of client-side genomic inference. While tailored for evolutionary analysis of selection and recombination, this browser-native architecture offers a generalizable blueprint for deploying complex bioinformatic tools without server-side dependencies.\n                    <jats:monospace>Datamonkey 3<\/jats:monospace>\n                    is freely available at\n                    <jats:ext-link>https:\/\/v3.datamonkey.org<\/jats:ext-link>\n                    , and all source code is available from\n                    <jats:ext-link>https:\/\/github.com\/veg\/datamonkey3<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.3389\/fbinf.2026.1876305","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T05:58:47Z","timestamp":1788933527000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Datamonkey 3: browser-native molecular evolution analysis"],"prefix":"10.3389","volume":"6","author":[{"given":"Steven","family":"Weaver","sequence":"first","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine, Temple University","place":["Philadelphia, PA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben","family":"Murrell","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet","place":["Stockholm, Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anton","family":"Nekrutenko","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, The Pennsylvania State University","place":["University Park, PA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine, Temple University","place":["Philadelphia, PA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"B1","unstructured":"Aioli: framework for building fast genomics web tools with WebAssembly\n          \n          \n            \n              Aboukhalil\n              R."},{"key":"B2","volume-title":"Biowasm: WebAssembly Modules for Genomics","author":"Aboukhalil","year":""},{"key":"B3","volume-title":"Model Context Protocol","year":"2024"},{"key":"B4","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1145\/3062341.3062363","article-title":"Bringing the web up to speed with WebAssembly","volume-title":"Proceedings of the 38th ACM SIGPLAN Conference on Programming Language Design and Implementation","author":"Haas","year":"2017"},{"key":"B5","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"B6","doi-asserted-by":"publisher","first-page":"W395","DOI":"10.1093\/nar\/gkaa434","article-title":"The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update","volume":"48","author":"Jalili","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B7","doi-asserted-by":"publisher","first-page":"btae018","DOI":"10.1093\/bioinformatics\/btae018","article-title":"ViralWasm: a client-side user-friendly web application suite for viral genomics","volume":"40","author":"Ji","year":"2024","journal-title":"Bioinformatics"},{"key":"B8","doi-asserted-by":"crossref","DOI":"10.64898\/2026.03.09.710461","volume-title":"Characterizing physicochemical selection in protein evolution with property-informed models (PRIME)","author":"Kim","year":"2026"},{"key":"B9","doi-asserted-by":"publisher","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","article-title":"Datamonkey: rapid detection of selective pressure on individual sites of codon alignments","volume":"21","author":"Kosakovsky Pond","year":"","journal-title":"Bioinformatics"},{"key":"B10","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not so different after all: a comparison of methods for detecting amino acid sites under selection","volume":"22","author":"Kosakovsky Pond","year":"","journal-title":"Mol. 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