ArticleBioinformatics advances2021
App-SpaM: phylogenetic placement of short reads without sequence alignment.
Article in Bioinformatics advances, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Identification of bacterial candidates that promote the growth of the seagrassbioRxiv : the preprint server for biology · 2026Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.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
- Functionally distinct core microbes of Tricholoma matsutake revealed by cross-study analysis.Microbiome · 2026Article
- Deconvolving Phylogenetic Distance Mixtures.bioRxiv : the preprint server for biology · 2026Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics.PLoS computational biology · 2025Article
- Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation.Ecology and evolution · 2025Article
- CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing.Bioinformatics (Oxford, England) · 2024Article
- Robust expansion of phylogeny for fast-growing genome sequence data.PLoS computational biology · 2024Article
- EPIK: precise and scalable evolutionary placement with informative k-mers.Bioinformatics (Oxford, England) · 2023Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Phylogenetic placement is the task of placing a query sequence of unknown taxonomic origin into a given phylogenetic tree of a set of reference sequences. A major field of application of such methods is, for example, the taxonomic identification of reads in metabarcoding or metagenomic studies. Several approaches to phylogenetic placement have been proposed in recent years. The most accurate of them requires a multiple sequence alignment of the references as input. However, calculating multiple alignments is not only time-consuming but also limits the applicability of these approaches. Results: Herein, we propose Availability and implementation: The source code of Contact: matthias.blanke@biologie.uni-goettingen.de. Supplementary information: Supplementary data are available at
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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.