The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes
Open accessAbstract
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.
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Cites
Goecks, J., Nekrutenko, A., Taylor, J., & The Galaxy Team (2010) · Genome Biology · doi:10.1186/gb-2010-11-8-r86 · Cited by 3,453
HyPhy: hypothesis testing using phylogenies
Pond, S. L. K., Frost, S. D. W., & Muse, S. V. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti079 · Cited by 2,866
Self-citationNot So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
Kosakovsky Pond, S. L., & Frost, S. D. W. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi105 · Cited by 2,324
Self-citationDetecting Individual Sites Subject to Episodic Diversifying Selection
Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Kosakovsky Pond, S. L. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002764 · Cited by 1,811
FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection
Murrell, B., Moola, S., Mabona, A., Weighill, T., Sheward, D., Kosakovsky Pond, S. L., & Scheffler, K. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst030 · Cited by 1,358
Self-citationDatamonkey: rapid detection of selective pressure on individual sites of codon alignments
Pond, S. L. K., & Frost, S. D. W. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti320 · Cited by 1,354
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm
Kosakovsky Pond, S. L., Posada, D., Gravenor, M. B., Woelk, C. H., & Frost, S. D. W. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl051 · Cited by 945
Self-citationSmith, M. D., Wertheim, J. O., Weaver, S., Murrell, B., Scheffler, K., & Kosakovsky Pond, S. L. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv022 · Cited by 811
Self-citationRELAX: Detecting Relaxed Selection in a Phylogenetic Framework
Wertheim, J. O., Murrell, B., Smith, M. D., Kosakovsky Pond, S. L., & Scheffler, K. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu400 · Cited by 778
Best Practices for Scientific Computing
Wilson, G., Aruliah, D. A., Brown, C. T., Chue Hong, N. P., Davis, M., Guy, R. T., Haddock, S. H. D., Huff, K. D., Mitchell, I. M., Plumbley, M. D., et al. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001745 · Cited by 723
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Kistler, K. E., & Bedford, T. (2021) · eLife · doi:10.7554/elife.64509 · Cited by 94
Evolutionary dynamics of the chromatophore genome in three photosynthetic Paulinella species
Lhee, D., Ha, J.-S., Kim, S., Park, M. G., Bhattacharya, D., & Yoon, H. S. (2019) · Scientific Reports · doi:10.1038/s41598-019-38621-8 · Cited by 54
Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life
Bredon, M., Herran, B., Lheraud, B., Bertaux, J., Grève, P., Moumen, B., & Bouchon, D. (2019) · BMC Genomics · doi:10.1186/s12864-019-5825-8 · Cited by 36
Schaschl, H., & Wallner, B. (2020) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1575-0 · Cited by 24
Recognition and cleavage of human tRNA methyltransferase TRMT1 by the SARS-CoV-2 main protease
D'Oliviera, A., Dai, X., Mottaghinia, S., Olson, S., Geissler, E. P., Etienne, L., Zhang, Y., & Mugridge, J. S. (2025) · eLife · doi:10.7554/elife.91168.3 · Cited by 13
Metadata
- Authors
- Weaver, S., Shank, S. D., Spielman, S. J., Li, M., Muse, S. V., & Kosakovsky Pond, S. L.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-01-02
- Volume
- 35
- Issue
- 3
- Pages
- 773-777
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2781938185
- Cited by
- 983
- References
- 27
- FWCI
- 17.76
- Type
- journal article
- Language
- en
- Open access
- green
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