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SEPP: SATé-Enabled Phylogenetic Placement
Abstract
We address the problem of Phylogenetic Placement, in which the objective is to insert short molecular sequences (called query sequences) into an existing phylogenetic tree and alignment on full-length sequences for the same gene. Phylogenetic placement has the potential to provide information beyond pure "species identification" (i.e., the association of metagenomic reads to existing species), because it can also give information about the evolutionary relationships between these query sequences and to known species. Approaches for phylogenetic placement have been developed that operate in two steps: first, an alignment is estimated for each query sequence to the alignment of the full-length sequences, and then that alignment is used to find the optimal location in the phylogenetic tree for the query sequence. Recent methods of this type include HMMALIGN+EPA, HMMALIGN+pplacer, and PaPaRa+EPA.We report on a study evaluating phylogenetic placement methods on biological and simulated data. This study shows that these methods have extremely good accuracy and computational tractability under conditions where the input contains a highly accurate alignment and tree for the full-length sequences, and the set of full-length sequences is sufficiently small and not too evolutionarily diverse; however, we also show that under other conditions accuracy declines and the computational requirements for memory and time exceed acceptable limits. We present SEPP, a general "boosting" technique…
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“The state-of-the-art method for building phylogenetic trees from alignments has been shown to be outperformed on gut microbiome data by the placement of the sequences into an existing tree with SEPP35,36, which, when sufficient data are available, outperforms de novo phylogeny estimation from alignments36.”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [35]
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Metadata
- Authors
- MIRARAB, S., NGUYEN, N., & WARNOW, T.
- Affiliations
- The University of Texas at Austin (US)
- Venue
- Biocomputing 2012
- Publisher
- WORLD SCIENTIFIC
- Published
- 2011-12
- Pages
- 247-258
- OpenAlex
- W2033900229
- Cited by
- 251
- References
- 0
- Citations by year
- 2026: 13 · 2025: 34 · 2024: 27 · 2023: 37 · 2022: 43 · 2021: 26 · 2020: 14 · 2019: 11 · 2018: 17 · 2017: 3 · 2016: 4 · 2015: 4 · 2014: 4 · 2013: 8 · 2012: 6
- FWCI
- 21.13
- Type
- conference paper
- Language
- en
- Open access
- closed
- Locations
- Pacific Symposium on Biocomputing (PSB) (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- phylogenetic placement, sate, boosting, computational tractability
- MeSH terms
- Algorithms, Bacteria, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Software, Sequence Alignment, Evolution, Molecular, Computational Biology, Databases, Nucleic Acid, Metagenome, Metagenomics
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