Other Access

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

JSON RDF

myPhyloDB

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).

Dataset Info

These fields are compatible with DCAT, an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.
FieldValue
Authors
Manter, Daniel
(ORCID)
Product Type
Software tool
Intended Use
An open-source software package for accessing and analyzing microbial ecology data via a user-friendly web-interface.
Publisher
Agricultural Research Service
Contact Name
Manter, Daniel
Contact Email
Public Access Level
Public
Primary Article

Manter, D. K., Korsa, M., Tebbe, C., & Delgado, J. A. (2016). MyPhyloDB: A local web server for the storage and analysis of metagenomic data. Database, doi:10.1093/database/baw037

Is Part Of
Related Content
License
Funding Source(s)
Agricultural Research Service
Program Code
005:037 - Department of Agriculture - Research and Education
Bureau Code
005:18 - Agricultural Research Service
Modified Date
2019-05-07
Release Date
2018-07-05
Ag Data Commons Keywords: 
  • Agroecosystems & Environment
  • Soil
  • Biogeochemistry
  • Agroecosystems & Environment
  • Water
  • Agroecosystems & Environment
  • Soil
  • Agroecosystems & Environment
  • Microbial ecology
  • Genomics & Genetics
  • Metagenomics
  • Genomics & Genetics
  • Agroecosystems & Environment
  • Online database