ArticleBMC genomics2010
MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- Binning Metagenomic Contigs Using Unsupervised Clustering and Reference Databases.Interdisciplinary sciences, computational life sciences · 2022Article
- Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- MetaCRS: unsupervised clustering of contigs with the recursive strategy of reducing metagenomic dataset's complexity.BMC bioinformatics · 2022Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler.Bioinformatics (Oxford, England) · 2020Article
- Phylogenetic double placement of mixed samples.Bioinformatics (Oxford, England) · 2020Article
- APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments.Systematic biology · 2020Article
- Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?IMA fungus · 2020Article
- Formal description of sequence-based voucherlessIMA fungus · 2018Article
- Colorful seashells: Identification of haem pathway genes associated with the synthesis of porphyrin shell color in marine snails.Ecology and evolution · 2017Article
- A clinician's guide to microbiome analysis.Nature reviews. Gastroenterology & hepatology · 2017Review
- Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes.Royal Society open science · 2017Article
- A Metagenomic Approach to Cyanobacterial Genomics.Frontiers in microbiology · 2017Review
- LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes.Bioinformatics (Oxford, England) · 2016Article
- HPV16 variants distribution in invasive cancers of the cervix, vulva, vagina, penis, and anus.Cancer medicine · 2016Article
- MBMC: An Effective Markov Chain Approach for Binning Metagenomic Reads from Environmental Shotgun Sequencing Projects.Omics : a journal of integrative biology · 2016Article
- Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis.Evolutionary bioinformatics online · 2016Review
- Metabarcoding of marine nematodes - evaluation of reference datasets used in tree-based taxonomy assignment approach.Biodiversity data journal · 2016Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundShotgun 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.
resultsExisting 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.
conclusionsWe discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.