Main logo
tutorial arrow
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

phyloseq | An R package for reproducible interactive analysis and graphics of microbiome census data

A package dedicated to the object-oriented representation and analysis of microbiome census data in R. Phyloseq supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics, all in a manner that is easy to document, share, and modify. It simplifies many of the common data management and preprocessing tasks required during analysis of phylogenetic sequencing data. The phyloseq package also provides a set of powerful analysis and graphics functions, building upon related packages available in R and Bioconductor. It includes or supports some of the most commonly-needed ecology and phylogenetic tools, including a consistent interface for calculating ecological distances and performing dimensional reduction.

User report

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

No review has been posted.

phyloseq forum

tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

phyloseq classification

phyloseq specifications

Unique identifier:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
GNU Affero General Public License version 3
Software type:
Restrictions to use:
Programming languages:
Computer skills:

phyloseq distribution


tutorial arrow
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

phyloseq support



  • Paul J. McMurdie <>


tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship



Department of Statistics, Stanford University, Stanford, CA, USA; The Roslin Institute, University of Edinburgh, UK

Funding source(s)

This work was supported by grant NIH-R01GM086884.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.