ArticlePLoS computational biology2026
TIPP-SD: A new method for species detection in microbiomes.
Article in PLoS computational biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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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.
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4 authors.
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Abstract
In this study, we present TIPP-SD (i.e., TIPP for Species Detection), a new technique for species detection in a microbiome sample. TIPP-SD uses a substantially modified version of TIPP3, which is a recently developed abundance profiling tool based on maximum likelihood phylogenetic placement into marker gene taxonomies. TIPP-SD depends on a parameter (i.e., "threshold") for the required support for species detection, thus allowing us to compute a precision-recall curve as we vary this parameter. In comparing the precision-recall curves for TIPP-SD, TIPP3, Kraken2, Bracken, Metabuli, and Metapresence, we find that TIPP-SD improves on the other methods with respect to accuracy under conditions where there is a highly variable distribution of species abundance or where there is sequencing error. Under other conditions, TIPP-SD is close to the best of these methods. Finally, although TIPP-SD is slower than the other methods, it is still fast enough to be used on large datasets. TIPP-SD is available in github as part of the TIPP3 software package.
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