MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
Open Access
- 5 August 2010
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 11 (1), 461
- https://doi.org/10.1186/1471-2164-11-461
Abstract
Background: Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. Results: Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information. Conclusions: We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.Keywords
This publication has 71 references indexed in Scilit:
- A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaNature, 2009
- Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environmentApplied Microbiology and Biotechnology, 2009
- Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov modelsNature Methods, 2009
- A core gut microbiome in obese and lean twinsNature, 2008
- Mechanistic Diversity in the RuBisCO Superfamily: A Novel Isomerization Reaction Catalyzed by the RuBisCO-like Protein from Rhodospirillum rubrumBiochemistry, 2008
- Genomic sequencing of single microbial cells from environmental samplesCurrent Opinion in Microbiology, 2008
- Millimeter‐scale genetic gradients and community‐level molecular convergence in a hypersaline microbial matMolecular Systems Biology, 2008
- Use of simulated data sets to evaluate the fidelity of metagenomic processing methodsNature Methods, 2007
- Sequencing genomes from single cells by polymerase cloningNature Biotechnology, 2006
- Evolutionary trees from DNA sequences: A maximum likelihood approachJournal of Molecular Evolution, 1981