ArticleBioinformatics (Oxford, England)2019
Methods for automatic reference trees and multilevel phylogenetic placement.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Identification of a membrane transporter for dimethylsulfoniopropionate uptake in marine eukaryotic phytoplankton.Nature communications · 2026Article
- How Does Transcription-Associated Mutagenesis Shape tRNA Microevolution?Genome biology and evolution · 2026Article
- Getting to the root of HIV transmitted founder virus sequences.Virus evolution · 2026Article
- CRISPR/Cas9 Knockout of Shell Matrix Protein 1 in the Slipper-Snail Crepidula atrasolea.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Article
- Scalable method for exploring phylogenetic placement uncertainty with custom visualizations usingiMeta · 2025Article
- Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies.Scientific reports · 2023Article
- African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing.Scientific reports · 2022Article
- SHOOT: phylogenetic gene search and ortholog inference.Genome biology · 2022Article
- Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes.Frontiers in microbiology · 2022Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Type II Photosynthetic Reaction Center Genes of Avocado (Persea americana Mill.) Bark Microbial Communities are Dominated by Aerobic Anoxygenic Alphaproteobacteria.Current microbiology · 2021Article
- Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult.Molecular biology and evolution · 2021Article
- App-SpaM: phylogenetic placement of short reads without sequence alignment.Bioinformatics advances · 2021Article
- Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition.Nature communications · 2020Article
- TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler.Bioinformatics (Oxford, England) · 2020Article
- Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction.Molecular biology and evolution · 2020Article
- Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.Bioinformatics (Oxford, England) · 2020Article
- PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes.GigaScience · 2020Article
- CAMITAX: Taxon labels for microbial genomes.GigaScience · 2020Article
- The relationship between cigarette smoking and the tongue microbiome in an East Asian population.Journal of oral microbiology · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationIn most metagenomic sequencing studies, the initial analysis step consists in assessing the evolutionary provenance of the sequences. Phylogenetic (or Evolutionary) Placement methods can be employed to determine the evolutionary position of sequences with respect to a given reference phylogeny. These placement methods do however face certain limitations: The manual selection of reference sequences is labor-intensive; the computational effort to infer reference phylogenies is substantially larger than for methods that rely on sequence similarity; the number of taxa in the reference phylogeny should be small enough to allow for visually inspecting the results.
resultsWe present algorithms to overcome the above limitations. First, we introduce a method to automatically construct representative sequences from databases to infer reference phylogenies. Second, we present an approach for conducting large-scale phylogenetic placements on nested phylogenies. Third, we describe a preprocessing pipeline that allows for handling huge sequence datasets. Our experiments on empirical data show that our methods substantially accelerate the workflow and yield highly accurate placement results. AVAILABILITY AND IMPLEMENTATION: Freely available under GPLv3 at http://github.com/lczech/gappa. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.