The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
Open accessAbstract
Summary: With the explosive growth of bacterial and archaeal sequence data, large-scale phylogenetic analyses present both opportunities and challenges. Here we describe AMPHORA2, an automated phylogenomic inference tool that can be used for high-throughput, high-quality genome tree reconstruction and metagenomic phylotyping. Compared with its predecessor, AMPHORA2 has several major enhancements and new functions: it has a greatly expanded phylogenetic marker database and can analyze both bacterial and archaeal sequences; it incorporates probability-based sequence alignment masks that improve the phylogenetic accuracy; it can analyze DNA as well as protein sequences and is more sensitive in marker identification; finally, it is over 100× faster in metagenomic phylotyping. Availability: http://wolbachia.biology.virginia.edu/WuLab/Software.html. Contact: mw4yv@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Cited by
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496
The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624
Mutant phenotypes for thousands of bacterial genes of unknown function
Price, M. N., Wetmore, K. M., Waters, R. J., Callaghan, M., Ray, J., Liu, H., Kuehl, J. V., Melnyk, R. A., Lamson, J. S., Suh, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0124-0 · Cited by 576
Sun, Z., Harris, H. M. B., McCann, A., Guo, C., Argimón, S., Zhang, W., Yang, X., Jeffery, I. B., Cooney, J. C., Kagawa, T. F., et al. (2015) · Nature Communications · doi:10.1038/ncomms9322 · Cited by 543
Aguiar-Pulido, V., Huang, W., Suarez-Ulloa, V., Cickovski, T., Mathee, K., & Narasimhan, G. (2016) · Evolutionary Bioinformatics · doi:10.4137/ebo.s36436 · Cited by 499
Metadata
- Authors
- Wu, M., & Scott, A. J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-02-12
- Volume
- 28
- Issue
- 7
- Pages
- 1033-1034
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2112419798
- Cited by
- 452
- References
- 1
- FWCI
- 8.95
- Type
- journal article
- Language
- en
- Open access
- bronze
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