General Information
| Description | Diversity analysis of functional gene amplicons |
| Homepage | https://github.com/outbig/DAFGA |
Publications
DAFGA: diversity analysis of functional gene amplicons
Summary:
Diversity analysis of functional marker genes provides physiological insights into microbial guilds that perform an ecologically relevant process. However, it is challenging to group functional gene sequences to valid taxonomic units, primarily because of differences in the evolutionary rates of individual genes and possible horizontal gene transfer events. We developed a python script package named DAFGA, which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. As a result, DAFGA provides gene-specific parameter sets for operational taxonomic unit clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME.
Availability and implementation:
DAFGA is freely available with a manual and test data from https://github.com/outbig/DAFGA .
Contact:
yongkyu.kim@mpi-marburg.mpg.de
Related Tools
SPANNER
Published June 2013
Taxonomic assignment of sequences using pyramid matching of similarity profiles
Quikr
Published June 2013
A method for rapid reconstruction of bacterial communities via compressive sensing
Taxator-tk
Published November 2014
Precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods
WormExp
Published November 2015
A web-based application for a Caenorhabditis elegans-specific gene expression enrichment analysis
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
