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posted on 2023-11-30, 08:15 authored by Daniel Manter

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).

Resources in this dataset:

  • Resource Title: Website Pointer to myPhyloDB.

    File Name: Web Page, url:

    Provides information and links to download latest version, release history, documentation, and tutorials including type of analysis you would like to perform (Univariate: ANCOVA/GLM; Multivariate: DiffAbund, PcoA, or sPLS).


Agricultural Research Service,


Data contact name

Manter, Daniel

Data contact email


Agricultural Research Service

Intended use

An open-source software package for accessing and analyzing microbial ecology data via a user-friendly web-interface.


  • Not specified

ISO Topic Category

  • biota
  • environment
  • farming

National Agricultural Library Thesaurus terms

agricultural management; agroecosystems; data collection; antibiotic resistance; databases; meta-analysis; computer software; data analysis; genetic databases; microbial ecology; information processing; analysis of covariance; least squares; soil biology; microbial communities; metagenomics; species diversity

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 211
  • 212

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Manter, Daniel (2018). myPhyloDB. Agricultural Research Service.