The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
How to Name and Classify Your Phage: An Informal Guide
Open accessAbstract
With this informal guide, we try to assist both new and experienced phage researchers through two important stages that follow phage discovery; that is, naming and classification. Providing an appropriate name for a bacteriophage is not as trivial as it sounds, and the effects might be long-lasting in databases and in official taxon names. Phage classification is the responsibility of the Bacterial and Archaeal Viruses Subcommittee (BAVS) of the International Committee on the Taxonomy of Viruses (ICTV). While the BAVS aims at providing a holistic approach to phage taxonomy, for individual researchers who have isolated and sequenced a new phage, this can be a little overwhelming. We are now providing these researchers with an informal guide to phage naming and classification, taking a “bottom-up” approach from the phage isolate level.
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MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst197 · Cited by 47,205
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.75 · Cited by 15,355
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357
Self-citationRoary: 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
Phylogeny.fr: robust phylogenetic analysis for the non-specialist
Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J.-F., Guindon, S., Lefort, V., Lescot, M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn180 · Cited by 4,700
NCBI BLAST: a better web interface
Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. L. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn201 · Cited by 4,232
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848
Easyfig: a genome comparison visualizer
Sullivan, M. J., Petty, N. K., & Beatson, S. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr039 · Cited by 3,583
Cited by
Phage diversity, genomics and phylogeny
Dion, M. B., Oechslin, F., & Moineau, S. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0311-5 · Cited by 960
Cook, R., Brown, N., Redgwell, T., Rihtman, B., Barnes, M., Clokie, M., Stekel, D. J., Hobman, J., Jones, M. A., & Millard, A. (2021) · PHAGE · doi:10.1089/phage.2021.0007 · Cited by 334
Cook, R., Hooton, S., Trivedi, U., King, L., Dodd, C. E. R., Hobman, J. L., Stekel, D. J., Jones, M. A., & Millard, A. D. (2021) · Microbiome · doi:10.1186/s40168-021-01010-3 · Cited by 319
Humolli, D., Piel, D., Maffei, E., Heyer, Y., Agustoni, E., Shaidullina, A., Willi, L., Imwinkelried, P., Estermann, F., Cuénod, A., et al. (2025) · PLOS Biology · doi:10.1371/journal.pbio.3003063 · Cited by 36
Veldsman, W. P., Yang, C., Zhang, Z., Huang, Y., Chowdhury, D., & Zhang, L. (2024) · Viruses · doi:10.3390/v16010134 · Cited by 2
Metadata
- Authors
- Adriaenssens, E., & Brister, J. R.
- Venue
- Viruses
- Publisher
- MDPI AG
- Published
- 2017-04-03
- Volume
- 9
- Issue
- 4
- Pages
- 70
- ISSN
- 1999-4915 (ISSN-L)
- OpenAlex
- W2949853177
- Cited by
- 477
- References
- 30
- FWCI
- 22.85
- Type
- journal article
- Language
- en
- Open access
- gold
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