phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
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Article on Improved Microbiome Analysis

McMurdie and Holmes (2014) Waste Not, Want Not: Why Rarefying Microbiome Data is Statistically Inadmissible PLoS Computational Biology 10(4): e1003531

Presubmission versions ahead of acceptance (2013): PDF version 2, PDF version 1

Peer-reviewed articles about phyloseq

McMurdie and Holmes (2014) Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking. Bioinformatics (Oxford, England) 31(2), 282–283.

McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217

Other resources

The phyloseq project also has a number of supporting online resources, including (but probably not limited to)

the phyloseq home page

the phyloseq FAQ

I recommend checking this page, and the issues tracker, before posting new issues.

Bioconductor stable release.

the phyloseq Issue Tracker

This is the recommended location to post

(1) feature requests (2) bug reports (3) theoretical considerations (4) other issues, feedback (5) ask for help

Search previous posts, and check the phyloseq FAQ before posting a new issue.