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).

Data and Resources

Field Value
accessLevel public
bureauCode {005:18}
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catalog_describedBy https://project-open-data.cio.gov/v1.1/schema/catalog.json
identifier f3259a43-4930-43a8-837d-08d0d552ddb5
license https://creativecommons.org/publicdomain/zero/1.0/
modified 2021-10-07
programCode {005:040}
publisher Agricultural Research Service
resource-type Dataset
source_datajson_identifier true
source_hash 8708aa0ac61ecfde5f9ed1f39ecf9ecbc0490619
source_schema_version 1.1
Groups
  • AmeriGEOSS
  • National Provider
  • North America
Tags
  • agricultural-research-service
  • amerigeo
  • amerigeoss
  • ckan
  • geo
  • geoss
  • myphylodb
  • national
  • north-america
  • np211
  • np212
  • united-states
isopen True
license_id cc-zero
license_title Creative Commons CCZero
license_url http://www.opendefinition.org/licenses/cc-zero
maintainer Manter, Daniel
maintainer_email daniel.manter@ars.usda.gov
metadata_created 2025-11-20T23:13:03.734897
metadata_modified 2025-11-20T23:13:03.734900
notes <p>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.</p> <p>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).</p>
num_resources 1
num_tags 12
title myPhyloDB