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.
Keywords
Phylogenetic treeConstruct (python library)Computer scienceTree (set theory)UnixMaximum parsimonyVariety (cybernetics)BiologyGeneticsProgramming languageMathematicsCombinatoricsSoftwareCladeArtificial intelligence
Affiliated Institutions
Related Publications
The ribosomal database project
The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered ali...
IQPNNI: Moving Fast Through Tree Space and Stopping in Time
An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast al...
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Abstract Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies ...
Ultrafast Approximation for Phylogenetic Bootstrap
Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data,...
jModelTest: Phylogenetic Model Averaging
jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm...
Publication Info
- Year
- 1994
- Type
- article
- Volume
- 10
- Issue
- 1
- Pages
- 41-48
- Citations
- 1121
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
1121
OpenAlex
Cite This
Gary J. Olsen,
Hideo Matsuda,
R. Hagstrom
et al.
(1994).
fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.
Computer applications in the biosciences
, 10
(1)
, 41-48.
https://doi.org/10.1093/bioinformatics/10.1.41
Identifiers
- DOI
- 10.1093/bioinformatics/10.1.41