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Protocols

Pplacer specifications

Information


Unique identifier OMICS_01462
Name Pplacer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Pplacer

Pplacer citations

 (99)
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

[…] ATé-enabled phylogenetic placement (SEPP) (), which inserts fragment sequences into a large phylogeny using a divide-and-conquer approach, utilizing HMMER () to identify putative subtrees followed by pplacer for the actual fragment placement. We benchmarked SEPP using 16S V4 sequence fragments and showed that it outperforms the present “state-of-the-art” approach of reconstructing de novo phylogen […]

library_books

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

2018
Appl Environ Microbiol
PMCID: 5861821
PMID: 29427429
DOI: 10.1128/AEM.02627-17

[…] equence databases and phylogenetic information to give a more accurate picture of the relative abundances of these OTUs. These include Copyrighter (), rrNDB (), functions in the picante R package and pplacer (), and part of the PICRUSt package ().As these techniques are reliant on databases, the same problems are present as for taxonomic identification. Principally, lesser-studied bacterial taxono […]

call_split

Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils

2018
Sci Rep
PMCID: 5856767
PMID: 29549345
DOI: 10.1038/s41598-018-23032-y
call_split See protocol

[…] he R package ggplot2 v. 2.1.0 and the Archaeopteryx tree viewer v. 0.9920. nrfA phylogenetic tree with edges fattened in proportion to the number of reads was made for natural site by guppy tool from pplacer suite. BWPD indices, which account for abundance and are robust to sampling depth differences between samples, were computed at theta 0.5 for each N-cycling gene to investigate the diversity o […]

library_books

Microbial metagenome of urinary tract infection

2018
Sci Rep
PMCID: 5847550
PMID: 29531289
DOI: 10.1038/s41598-018-22660-8

[…] elihood reference tree was inferred under the general time-reversible model with gamma-distributed rate heterogeneity (GTR + Γ) using FastTree. The 16S reads were mapped onto the reference tree using pplacer with the default settings. The number of sequences assigned to each node on the reference tree was normalized to the total number of sequences from the corresponding samples. The normalized ab […]

call_split

Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis

2018
PLoS One
PMCID: 5830298
PMID: 29489859
DOI: 10.1371/journal.pone.0192443
call_split See protocol

[…] oject naïve Bayesian classifier []. Operational taxonomic units (OTUs) were defined at 97% similarity using average neighbor joining.Species-level classification for Streptococcus was performed using pplacer software package [, ]. Briefly, streptococci sequences were acquired via get.lineage command in mothur, and each sequence was then placed on a phylogenetic reference tree, which was generated […]

call_split

Long term use of cover crops and no till shift soil microbial community life strategies in agricultural soil

2018
PLoS One
PMCID: 5814021
PMID: 29447262
DOI: 10.1371/journal.pone.0192953
call_split See protocol

[…] ria and archaea with known trait values, and the reliability of the trait estimates was tested as described in Gravuer and Eskelinen (2017) []. Briefly, OTUs were placed onto the reference tree using pplacer software [] and rRNA gene copy number and genome size values were estimated for each placed OTU using picante:phyEstimate []. This method does not directly rely on OTU taxonomic assignments to […]

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Pplacer institution(s)
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

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