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phyloseq specifications


Unique identifier OMICS_01520
Name phyloseq
Alternative name Shiny-phyloseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Affero General Public License version 3
Computer skills Advanced
Stability Stable
R, ade4, ape, Biobase, BiocGenerics, biomformat, Biostrings, cluster, data.table, foreach, ggplot2, igraph, methods, multtest, plyr, reshape2, scales, vegan, BiocStyle, DESeq2, genefilter, knitr, metagenomeSeq, rmarkdown, testthat
Maintained Yes




No version available



  • person_outline Paul J. McMurdie

Publications for phyloseq

phyloseq citations


Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum

PMCID: 5952429
PMID: 29764499
DOI: 10.1186/s40168-018-0472-x

[…] Alpha diversity metrics (richness and Shannon’s index) were calculated using the phyloseq R package based on rarefied OTU counts. Pielou’s evenness index was calculated as Shannon’s index/ln (richness). The cross-sectional difference in alpha diversity between groups during pregna […]


Microbiota modification by probiotic supplementation reduces colitis associated colon cancer in mice

PMCID: 5949713
PMID: 29760543
DOI: 10.3748/wjg.v24.i18.1995
call_split See protocol

[…] eline[], using the USEARCH v9.2.64 package. For OTU clustering a threshold of 97% similarity was used through the UPARSE-OTU algorithm. α- and β-diversity analyses were calculated using the R package Phyloseq v.1.19.1[] and vegan 2.4_2 packets, using the OTU table normalized to the smallest sample size. Taxa with differential abundance between groups were identified using the Kruskal-Wallis test ( […]


The influence of oxygen and methane on nitrogen fixation in subarctic Sphagnum mosses

PMCID: 5936483
PMID: 29730829
DOI: 10.1186/s13568-018-0607-2
call_split See protocol

[…] age). All graphs were constructed in R using ggplot2.For downstream analysis of the community composition the OTU table and taxonomy files generated by Mothur, were imported into R and analyzed using phyloseq (McMurdie and Holmes ). […]


Climate driven shifts in sediment chemistry enhance methane production in northern lakes

Nat Commun
PMCID: 5935729
PMID: 29728566
DOI: 10.1038/s41467-018-04236-2

[…] nces were merged using Pandaseq and further quality filtered and taxonomy was assigned from the Green Genes database using Usearch v8.1.1861 and QIIME, respectively–. Data were analyzed in R with the Phyloseq package, and abundance data were corrected using the DeSEq2 package in R,. PCR was used on representative samples using the dsrA primers DSR1-F (5′-ACSCACTGGAAGCACGGCGG-3′) and DSR-R (5′-GTGG […]


Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

Front Microbiol
PMCID: 5938605
PMID: 29765359
DOI: 10.3389/fmicb.2018.00803

[…] ce among samples using “betadisper” as implemented in the R package vegan (Oksanen et al., ). We visualized relative abundances of bacteria in paired sample types using the “plot_heatmap” function in phyloseq v. 1.22.3, and visualized ordination plots using Principle Coordinate Analysis (PCoA). Finally, we used R packages vegan v. 2.4-5 (Dixon, ) and phytools v. 0.6-44 (Revell, ) to test for phylo […]


Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes

Front Microbiol
PMCID: 5938556
PMID: 29765370
DOI: 10.3389/fmicb.2018.00870

[…] Bray–Curtis dissimilarities between pig stables and associated farmer’s homes (i.e., the sample pair reflecting where a given farmer worked and lived) were calculated using the “distance” function in phyloseq version 1.16.2. The similarity between each associated stable–home pair was ranked among all non-matching stable–home pairs, with the resulting rank reflecting how similar associated stable–h […]


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phyloseq institution(s)
Department of Statistics, Stanford University, Stanford, CA, USA
phyloseq funding source(s)
Supported by National Institutes of Health [grant number R01-GM086884.

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