Software

16Stimator

Generate 16S rRNA gene (16S) copy number estimates for bacterial genomes based on comparison of sequencing read depths of ribosomal and single copy gene regions. Find more information about the development of the 16Stimator pipeline in our blog post. The method is published in:
Perisin et al. 2015. Unfortunately, the publication is not open access (please e-mail to retrieve a copy) but the code of 16Stimator is freely available.

MARTA – Metagenomic and rDNA Taxonomic Assignment

Phylogenetically classifies DNA sequence data using the nucleotide database and Taxonomy database from NCBI. The java-based software blasts each sequence that you provide and looks for a consensus taxon among the top-hits returned from blast. The software suite is published in Horton et al. 2010. and an example can be found in the supplements of the publication (download pdf). Here are more information on installation and usage of MARTA.

Effectorsearch

Quickly and effectively identify candidate type III secretion system effectors in bacterial genomes. Download the compressed file archive here. It contains all scripts and dependencies as well as the text file Manual with instructions on installation and the contact details of developer Wen Zhang.

University of Chicago, Dept. of Ecology & Evolution