The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction
Abstract
Genome-based phylogeny plays a central role in the future taxonomy and phylogenetics of Bacteria and Archaea by replacing 16S rRNA gene phylogeny. The concatenated core gene alignments are frequently used for such a purpose. The bacterial core genes are defined as single-copy, homologous genes that are present in most of the known bacterial species. There have been several studies describing such a gene set, but the number of species considered was rather small. Here we present the up-to-date bacterial core gene set, named UBCG, and software suites to accommodate necessary steps to generate and evaluate phylogenetic trees. The method was successfully used to infer phylogenomic relationship of Escherichia and related taxa and can be used for the set of genomes at any taxonomic ranks of Bacteria. The UBCG pipeline and file viewer are freely available at https://www.ezbiocloud.net/tools/ubcg and https://www.ezbiocloud.net/tools/ubcg_viewer , respectively.
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Felsenstein, J. (1985) · Evolution · doi:10.1111/j.1558-5646.1985.tb00420.x · Cited by 44,647
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Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
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Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,587
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Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D. R., da Costa, M. S., Rooney, A. P., Yi, H., Xu, X.-W., De Meyer, S., et al. (2018) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.002516 · Cited by 3,081
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Metadata
- Authors
- Na, S.-I., Kim, Y. O., Yoon, S.-H., Ha, S.-M., Baek, I., & Chun, J.
- Venue
- Journal of Microbiology
- Publisher
- The Microbiological Society of Korea
- Published
- 2018-02-28
- Volume
- 56
- Issue
- 4
- Pages
- 280-285
- ISSN
- 1225-8873 (ISSN-L)
- 1976-3794
- OpenAlex
- W2791279372
- Cited by
- 1,373
- References
- 27
- FWCI
- 39.71
- Type
- journal article
- Language
- en
- Open access
- closed
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- Na, S.-I., Kim, Y. O., Yoon, S.-H., Ha, S.-M., Baek, I., & Chun, J. (2018). UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. Journal of Microbiology. https://doi.org/10.1007/s12275-018-8014-6
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