SEPP statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool SEPP

Tool usage distribution map

This map represents all the scientific publications referring to SEPP per scientific context
info info

Associated diseases


Popular tool citations

chevron_left Phylogenetic inference chevron_right
Want to access the full stats & trends on this tool?

SEPP specifications


Unique identifier OMICS_25055
Alternative name SATé-Enabled Phylogenetic Placement
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained No


No version available


This tool is not available anymore.

Publication for SATé-Enabled Phylogenetic Placement

SEPP citations


American Gut: an Open Platform for Citizen Science Microbiome Research

PMCID: 5954204
DOI: 10.1128/mSystems.00031-18

[…] les while the rest used 150. Following processing by Deblur, previously recognized bloom sequences were removed (). The Deblur sOTUs were inserted into the Greengenes 13_8 () 99% reference tree using SEPP (). SEPP uses the simultaneous alignment and tree estimation strategy described in reference to identify reasonable placements for sequence fragments within an existing phylogeny and alignment. […]


Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

PMCID: 5904434
PMID: 29719869
DOI: 10.1128/mSystems.00021-18

[…] CoA space (black arrow in ), where all sample data from the Yanomami study appear in a straight line.Insertion of the heterogeneous sOTU sequences from the two studies into the same backbone tree via SEPP resulted in a phylogeny that separated the samples as expected in the PCoA space corresponding to the body product data, where the differences between studies are small compared to differences am […]


KatharoSeq Enables High Throughput Microbiome Analysis from Low Biomass Samples

PMCID: 5864415
PMID: 29577086
DOI: 10.1128/mSystems.00218-17

[…] d trimmed to 150 bp and then processed with deblur (), a de novo sOTU picking method. For phylogenetics-based distance comparisons of the microbiomes, a tree was constructed from the sOTUs with SEPP (SATé-Enabled Phylogenetic Placement;, and then results were visualized in EMPeror (). Sample communities were then annotated with Greengenes. […]


HIPPI: highly accurate protein family classification with ensembles of HMMs

BMC Genomics
PMCID: 5123343
DOI: 10.1186/s12864-016-3097-0

[…] ved subfamily identification, and improved orthology detection [, , –].We have developed similar methods for representing a multiple sequence alignment with an ensemble of HMMs. These methods include SEPP [], TIPP [], and UPP [] (collectively referred to as the ∗PP methods). One of the key difference between the ∗PP methods and previous ensemble approaches (i.e., [, ]) is that the profile HMMs gen […]


High diversity of picornaviruses in rats from different continents revealed by deep sequencing

PMCID: 5034103
PMID: 27530749
DOI: 10.1038/emi.2016.90

[…] . For example, we also identified contigs with >70% identity to known rat-specific cardioviruses (). Expanding the analysis to other viral families could reveal further virome diversity.Likewise, the SEPP approach enabled placement of short contigs (>100 nt) into the picornavirus phylogeny. Almost all of the small contigs aligned with high confidence (HMMER e-value <10−5). In virus discovery studi […]


Analytical Tools and Databases for Metagenomics in the Next Generation Sequencing Era

PMCID: 3794082
PMID: 24124405
DOI: 10.5808/GI.2013.11.3.102

[…] ly to the low DB coverage, which is the case with microbial eukaryotes. Tools using phylogenetic methods in taxonomic assignment include the evolutionary placement algorithm (EPA) [], pplacer [], and SEPP [], and these algorithms were recently incorporated into QIIME [] and AMPHORA2 []. […]

Want to access the full list of citations?
SEPP institution(s)
Department of Computer Science, University of Texas at Austin, Austin, TX, USA

SEPP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SEPP