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The Ag Data Commons is migrating

The Ag Data Commons is migrating to a new institutional portal on Figshare. The current system is available for search and download only. The new platform is open for submission with assistance from Ag Data Commons curators. Please contact NAL-ADC-Curator@usda.gov, if you need to publish or update your datasets.

Other Access

The information on this page (the dataset metadata) is also available in these formats:


via the DKAN API


myPhyloDB is an open-source software package aimed at developing a user-friendly web-interface for accessing and analyzing all of your laboratory's microbial ecology data (currently supported project types: soil, air, water, microbial, and human-associated). The storage and handling capabilities of myPhyloDB archives users' raw sequencing files, and allows for easy selection of any combination of projects/samples from all of your projects using the built-in SQL database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload, storage, and analysis of pre-processed data or raw (454 or Illumina) data files using the built-in versions of Mothur and R. myPhyloDB is designed to run as a local web-server, which allows a single installation to be accessible to all of your laboratory members, regardless of their operating system or other hardware limitations. myPhyloDB includes an embedded copy of the popular Mothur program and uses a customizable batch file to perform sequence editing and processing. This allows myPhyloDB to leverage the flexibility of Mothur and allow for greater standardization of data processing and handling across all of your sequencing projects.

myPhyloDB also includes an embedded copy of the R software environment for a variety of statistical analyses and graphics. Currently, myPhyloDB includes analysis for factor or regression-based ANcOVA, principal coordinates analysis (PCoA), differential abundance analysis (DESeq), and sparse partial least-squares regression (sPLS).

Parent Record
Release Date
Agricultural Research Service
Contact Name
Manter, Daniel
Contact Email
Public Access Level
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service