ArticleBioinformatics (Oxford, England)2021
TIPP2: metagenomic taxonomic profiling using phylogenetic markers.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- TIPP-SD: A new method for species detection in microbiomes.PLoS computational biology · 2026Article
- krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.Genome biology · 2026Article
- Deconvolving Phylogenetic Distance Mixtures.bioRxiv : the preprint server for biology · 2026Article
- Review
- Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics.PLoS computational biology · 2025Article
- Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet.bioRxiv : the preprint server for biology · 2024Article
- Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes.PLoS computational biology · 2024Article
- CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing.Bioinformatics (Oxford, England) · 2024Article
- YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.Bioinformatics (Oxford, England) · 2024Article
- From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools.Microbial genomics · 2023Article
- SCAMPP+FastTree: improving scalability for likelihood-based phylogenetic placement.Bioinformatics advances · 2023Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Critical Assessment of Metagenome Interpretation: the second round of challenges.Nature methods · 2022Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Tapping the Role of Microbial Biosurfactants in Pesticide Remediation: An Eco-Friendly Approach for Environmental Sustainability.Frontiers in microbiology · 2021Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationMetagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample.
resultsWe present TIPP2, a marker gene-based abundance profiling method, which combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2 and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset. AVAILABILITY AND IMPLEMENTATION: The code for our method is freely available in open-source form at https://github.com/smirarab/sepp/blob/tipp2/README.TIPP.md. The code and procedure to create new reference packages for TIPP2 are available at https://github.com/shahnidhi/TIPP_reference_package. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.