Pplacer protocols

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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 in pipelines

 (8)
2018
PMCID: 5847550
PMID: 29531289
DOI: 10.1038/s41598-018-22660-8

[…] 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 […]

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

[…] 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 […]

2016
PMCID: 4931233
PMID: 27352007
DOI: 10.1038/ncomms12015

[…] lineage information; (4) no redundant sequences. 7,890 16s rrna sequences were retained for constructing the phylogenetic tree. multiple sequence alignment was performed using muscle. per the pplacer manual (http://matsen.github.io/pplacer/generated_rst/pplacer.html), the 16s rrna reference tree was constructed using fasttree with parameter ‘-nt –gtr' (ref. ). fasttree infers phylogenetic […]

2015
PMCID: 4304780
PMID: 25615446
DOI: 10.1371/journal.pone.0116271

[…] variation and an estimate of invariable sites (jtt + γ + i). after translation, the phylogenetic positions of each representative sequence for the otus were placed onto the reference tree using the pplacer software []., to determine whether a strain belonging to the sar116 group can produce dms from dmsp, the imcc1322 strain, which is one of two isolates belonging to sar116 [], was grown […]

2015
PMCID: 4558845
PMID: 26116918
DOI: 10.1093/gbe/evv124

[…] utilized to query each target genome and/or transcriptome. the hmm profiles, sequence alignments used to generate them and all sequence alignments, trees and phyml statistics files used during the pplacer profiling step have been made available on figshare (doi: 10.6084/m9.figshare.1412684)., we utilized prottest () to estimate the best-fitting model of amino acid replacement […]


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Pplacer in publications

 (79)
PMCID: 5904434
PMID: 29719869
DOI: 10.1128/mSystems.00021-18

[…] in . the latter approach works well for otus but is hindered for sotus by the absence of some taxa in the reference database. although sequence fragment insertion methods such as epa () and pplacer () exist, these methods have not been tested with sotus from high-throughput amplicon studies using insertion against a broad reference phylogeny. a recent advance was made with saté-enabled […]

PMCID: 5856767
PMID: 29549345
DOI: 10.1038/s41598-018-23032-y

[…] 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 […]

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

[…] 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 […]

PMCID: 5830298
PMID: 29489859
DOI: 10.1371/journal.pone.0192443

[…] 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 […]

PMCID: 5814021
PMID: 29447262
DOI: 10.1371/journal.pone.0192953

[…] 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 […]


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

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