Evidence map›Paper›PMID 42056687›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.

Eleanor Wedell, Chengze Shen, Tandy Warnow

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Eleanor WedellSiebel School of Computing and Data Science, University of Illinois Urbana-Champaign, Urbana, IL, USA.
Chengze ShenSiebel School of Computing and Data Science, University of Illinois Urbana-Champaign, Urbana, IL, USA.
Tandy WarnowSiebel School of Computing and Data Science, University of Illinois Urbana-Champaign, Urbana, IL, USA. warnow@illinois.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Phylogenetic placement is the problem of adding sequences to an existing phylogenetic tree. While many techniques have been developed for this problem, methods based on optimizing maximum likelihood, such as pplacer and EPA-ng, have been shown to provide the highest accuracy. Unfortunately, these methods are limited to at most moderately large placement trees due to their design. SCAMPP and Batch-SCAMPP are two methods that have been developed to improve the scalability of both pplacer and EPA-ng to very large trees, while maintaining high accuracy. Here, we describe these methods and show how to use them in two applications: metagenomics, including taxon identification and abundance profiling, and incrementally growing large trees. SCAMPP and Batch-SCAMPP are available in open-source form on GitHub and PyPI.

Indexed as

Computational BiologyMetagenomicsPhylogenySoftwareAlgorithmsLikelihood FunctionsSequence Analysis, DNAAbundance profilingEPA-ngLarge phylogeniesMaximum likelihoodMicrobiome analysisPhylogenetic placementPplacerTaxon identification

Identifiers

PMID42056687

What OpenQuestion holds

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Registered trials

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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.