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SEPP specifications

Information


Unique identifier OMICS_25055
Name SEPP
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

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Publication for SATé-Enabled Phylogenetic Placement

SEPP citations

 (6)
library_books

American Gut: an Open Platform for Citizen Science Microbiome Research

2018
mSystems
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. […]

library_books

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

2018
mSystems
PMCID: 5904434
PMID: 29719869
DOI: 10.1128/mSystems.00021-18

[…] The higher taxonomic resolution of sub-OTU methods, together with more-precise phylogenetic reconstruction techniques such as SEPP, can be leveraged by phylogenetic distance metrics to expose relevant ecological differences from the results obtained by traditional closed- or open- reference OTU picking. We exemplify this pot […]

library_books

KatharoSeq Enables High Throughput Microbiome Analysis from Low Biomass Samples

2018
mSystems
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; https://github.com/smirarab/sepp/blob/master/sepp/tree.py), and then results were visualized in EMPeror (). Sample communities were then annotated with Greengenes. […]

library_books

HIPPI: highly accurate protein family classification with ensembles of HMMs

2016
BMC Genomics
PMCID: 5123343
DOI: 10.1186/s12864-016-3097-0

[…] ry sequence is fragmentary. Thus, HIPPI enables highly accurate family identification of amino acid sequences, even for very challenging conditions.The key advance in HIPPI over previous ∗PP methods (SEPP, TIPP, and UPP) is the method used to construct the ensemble of HMMs used to represent a seed alignment. While the previous ∗PP methods differed in various respects in how they built their ensemb […]

library_books

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

2016
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 […]

library_books

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

2013
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 []. […]

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SEPP institution(s)
Department of Computer Science, University of Texas at Austin, Austin, TX, USA

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