What is 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. 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. 

Current version and download:

myPhyloDB v.1.2.0: Official download page         

Installation instruction can be found in the manual or here

Local server:

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.  Simply install myPhyloDB on a single machine and direct users, on your local intranet to the appropriate URL and they will have instant access to your personal version of myPhyloDB.  

Database and archival system:

myPhyloDB organizes all of your uploaded projects in two ways.  First, all files are archived in a centrally organized upload folder - no more hunting for those missing data files.  Second, all projects, and their associated metadata, are uploaded into a single SQL database for easy access to all of your data regardless of the specific project and/or run date.

Processing pipeline:

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.  

Analysis options:

myPhyloDB also included 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).  To request additional features please see our Forum or email the myPhyloDB team.

Source code:

myPhyloDB is open-source software and the code can be found here. If you run into any bugs or would like to request a feature, please post such on the issues page


Daniel Manter
Res. Soil Scientist
Soil Management and Sugar Beet Research Unit
Fort Collins, CO 80526
(970) 492-7255
or contact the myPhyloDB team: myphylodb@gmail.com