The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Phandango: an interactive viewer for bacterial population genomics
Open accessAbstract
Summary: Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner. Availability and implementation: Phandango is a web application freely available for use at www.phandango.net and includes a diverse collection of datasets as examples. Source code together with a detailed wiki page is available on GitHub at https://github.com/jameshadfield/phandango.
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PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089
Roary: rapid large-scale prokaryote pan genome analysis
Page, A. J., Cummins, C. A., Hunt, M., Wong, V. K., Reuter, S., Holden, M. T. G., Fookes, M., Falush, D., Keane, J. A., & Parkhill, J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv421 · Cited by 5,736
Croucher, N. J., Page, A. J., Connor, T. R., Delaney, A. J., Keane, J. A., Bentley, S. D., Parkhill, J., & Harris, S. R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1196 · Cited by 2,741
Self-citationRapid Pneumococcal Evolution in Response to Clinical Interventions
Croucher, N. J., Harris, S. R., Fraser, C., Quail, M. A., Burton, J., van der Linden, M., McGee, L., von Gottberg, A., Song, J. H., Ko, K. S., et al. (2011) · Science · doi:10.1126/science.1198545 · Cited by 886
Self-citationMicroreact: visualizing and sharing data for genomic epidemiology and phylogeography
Argimón, S., Abudahab, K., Goater, R. J. E., Fedosejev, A., Bhai, J., Glasner, C., Feil, E. J., Holden, M. T. G., Yeats, C. A., Grundmann, H., et al. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000093 · Cited by 732
Self-citationChewapreecha, C., Marttinen, P., Croucher, N. J., Salter, S. J., Harris, S. R., Mather, A. E., Hanage, W. P., Goldblatt, D., Nosten, F. H., Turner, C., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004547 · Cited by 218
Self-citationSequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
Lees, J. A., Vehkala, M., Välimäki, N., Harris, S. R., Chewapreecha, C., Croucher, N. J., Marttinen, P., Davies, M. R., Steer, A. C., Tong, S. Y. C., et al. (2016) · Nature Communications · doi:10.1038/ncomms12797 · Cited by 196
Self-citationDetection of recombination events in bacterial genomes from large population samples
Marttinen, P., Hanage, W. P., Croucher, N. J., Connor, T. R., Harris, S. R., Bentley, S. D., & Corander, J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr928 · Cited by 189
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Cited by
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread
David, S., Reuter, S., Harris, S. R., Glasner, C., Feltwell, T., Argimon, S., Abudahab, K., Goater, R., Giani, T., Errico, G., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0492-8 · Cited by 773
Self-citationA Mycobacterial Systems Resource for the Research Community
Judd, J. A., Canestrari, J., Clark, R., Joseph, A., Lapierre, P., Lasek-Nesselquist, E., Mir, M., Palumbo, M., Smith, C., Stone, M., et al. (2021) · mBio · doi:10.1128/mbio.02401-20 · Cited by 45
Genomic convergence between Akkermansia muciniphila in different mammalian hosts
Geerlings, S. Y., Ouwerkerk, J. P., Koehorst, J. J., Ritari, J., Aalvink, S., Stecher, B., Schaap, P. J., Paulin, L., de Vos, W. M., & Belzer, C. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02360-6 · Cited by 28
Comparative Genomics and Pan-Genome Driven Prediction of a Reduced Genome of Akkermansia muciniphila
Bukhari, S. A. R., Irfan, M., Ahmad, I., & Chen, L. (2022) · Microorganisms · doi:10.3390/microorganisms10071350 · Cited by 18
Bhattacharya, A., Das, S., Bhattacharjee, M. J., Mukherjee, A. K., & Khan, M. R. (2023) · BMC Genomics · doi:10.1186/s12864-023-09665-y · Cited by 16
“Phandango [54] was used for proper visualization of the pangenome.”
Method
Metadata
- Authors
- Hadfield, J., Croucher, N. J., Goater, R. J., Abudahab, K., Aanensen, D. M., & Harris, S. R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-09-25
- Volume
- 34
- Issue
- 2
- Pages
- 292-293
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2949182334
- Cited by
- 659
- References
- 9
- FWCI
- 15.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Hadfield, J., Croucher, N. J., Goater, R. J., Abudahab, K., Aanensen, D. M., & Harris, S. R. (2018). Phandango: an interactive viewer for bacterial population genomics. Bioinformatics. https://doi.org/10.1093/bioinformatics/btx610
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