DAFGA: diversity analysis of functional gene amplicons

Bioinformatics. 2014 Oct;30(19):2820-1. doi: 10.1093/bioinformatics/btu394. Epub 2014 Jun 17.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cluster Analysis*
  • Computational Biology / methods*
  • Evolution, Molecular
  • Genes, rRNA*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics*
  • Software

Substances

  • RNA, Ribosomal, 16S