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fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
Abstract
We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on a wide variety of computers ranging from Unix workstations to massively parallel systems, and is available from the Ribosomal Database Project (RDP) by anonymous FTP. Our program uses a maximum likelihood approach and is based on version 3.3 of Felsenstein's dnaml program. Several enhancements, including algorithmic changes, significantly improve performance and reduce memory usage, making it feasible to construct even very large trees. Trees containing 40-100 taxa have been easily generated, and phylogenetic estimates are possible even when hundreds of sequences exist. We are currently using the tool to construct a phylogenetic tree based on 473 small subunit rRNA sequences from prokaryotes.
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Cited by
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
A likelihood approach to estimating phylogeny from discrete morphological character data
Lewis, P. O. (2001) · Systematic Biology · doi:10.1080/106351501753462876 · Cited by 2,929
Lanciotti, R. S., Roehrig, J. T., Deubel, V., Smith, J., Parker, M., Steele, K., Crise, B., Volpe, K. E., Crabtree, M. B., Scherret, J. H., et al. (1999) · Science · doi:10.1126/science.286.5448.2333 · Cited by 1,593
Timing the ancestor of the HIV-1 pandemic strains.
Korber, B., Muldoon, M., Theiler, J., Gao, F., Gupta, R., Lapedes, A., Hahn, B. H., Wolinsky, S., & Bhattacharya, T. (2000) · Science · doi:10.1126/science.288.5472.1789 · Cited by 1,021
Robertson, D. L., Anderson, J. P., Bradac, J. A., Carr, J. K., Foley, B., Funkhouser, R. K., Gao, F., Hahn, B. H., Kalish, M. L., Kuiken, C., et al. (2000) · Science · doi:10.1126/science.288.5463.55d · Cited by 964
Metadata
- Authors
- Olsen, G. J., Matsuda, H., Hagstrom, R., & Overbeek, R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 1994
- Volume
- 10
- Issue
- 1
- Pages
- 41-48
- ISSN
- 0266-7061 (ISSN-L)
- 1367-4803
- 1460-2059
- OpenAlex
- W2105926960
- Cited by
- 1,108
- References
- 0
- FWCI
- 22.55
- Type
- journal article
- Language
- en
- Open access
- closed
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- CoChat. (2026). Citation check: fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. https://app.cochat.ai/papers/10.1093/bioinformatics/10.1.41
- The paper
- Olsen, G. J., Matsuda, H., Hagstrom, R., & Overbeek, R. (1994). fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Bioinformatics. https://doi.org/10.1093/bioinformatics/10.1.41
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
