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Treffer: Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes.

Title:
Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes.
Authors:
Weaver S; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA., Shank SD; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA., Spielman SJ; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA., Li M; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA., Muse SV; Department of Statistics, North Carolina State University, Raleigh, NC., Kosakovsky Pond SL; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.
Source:
Molecular biology and evolution [Mol Biol Evol] 2018 Mar 01; Vol. 35 (3), pp. 773-777.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: PubMed not MEDLINE; MEDLINE
Imprint Name(s):
Publication: 2003- : New York, NY : Oxford University Press
Original Publication: [Chicago, Ill.] : University of Chicago Press, [c1983-
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Grant Information:
R01 AI134384 United States AI NIAID NIH HHS; R01 GM093939 United States GM NIGMS NIH HHS; U01 GM110749 United States GM NIGMS NIH HHS
Contributed Indexing:
Keywords: evolutionary inference; natural selection; recombination; statistical methods; web application
Entry Date(s):
Date Created: 20180105 Latest Revision: 20200306
Update Code:
20250114
PubMed Central ID:
PMC5850112
DOI:
10.1093/molbev/msx335
PMID:
29301006
Database:
MEDLINE

Weitere Informationen

Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data. For this endeavor, we leveraged recent developments in open-source libraries that facilitate interactive, robust, and scalable web application development. Datamonkey 2.0 provides a carefully curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. To complement Datamonkey 2.0, we additionally release HyPhy Vision, an accompanying JavaScript application for visualizing analysis results. HyPhy Vision can also be used separately from Datamonkey 2.0 to visualize locally executed HyPhy analyses. Together, Datamonkey 2.0 and HyPhy Vision showcase how scientific software development can benefit from general-purpose open-source frameworks. Datamonkey 2.0 is freely and publicly available at http://www.datamonkey.org, and the underlying codebase is available from https://github.com/veg/datamonkey-js.
(© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)