SEPP: SATe -Enabled Phylogenetic Placement

By Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow. 2011

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “These misalign-ments are due to an incorrect assumption on phylogenetic placement of new sequences shown in ﬁgure 1 C .”
American Gut: an Open Platform for Citizen Science Microbiome Research (2018, unknown): “Inserting the sOTU fragments of AGP and EMP samples into a Greengenes (19) reference phylogenetic tree using SATé-enabled Phylogenetic Placement (SEPP) (20) (Fig.”
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information (2018, methodology): “These choices are driven by computational constraints; increasing the placement subset size (which is in theory desirable) puts a high burden on the memory, and reducing the alignment subset could increase the running time with minor improvements in the accuracy of results (9) (see Fig.”
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes (2021, methodology): “This is achieved through the phylogenetic placement of the input sequence (genome, gene set, or transcriptome) on a set of precomputed phylogenetic trees using SEPP (Mirarab et al. 2011) and pplacer (Matsen et al. 2010).”
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm (2012, background): “Received on January 5, 2012; revised on April 13, 2012; accepted on April 16, 2012”