Cited by 252Genomics and Phylogenetic StudiesRNA and protein synthesis mechanismsFractal and DNA sequence analysis

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SEPP: SATé-Enabled Phylogenetic Placement

MIRARAB, S., NGUYEN, N., WARNOW, T.·2011·Biocomputing 2012

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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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Authors: MIRARAB, S., NGUYEN, N., & WARNOW, T.
Affiliations: The University of Texas at Austin (US)
ORCID: MIRARAB, S.
NGUYEN, N.
WARNOW, T.
Venue: Biocomputing 2012
Publisher: WORLD SCIENTIFIC
Published: 2011-12
Pages: 247-258
DOI: 10.1142/9789814366496_0024
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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SEPP: SATé-Enabled Phylogenetic Placement

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