Shigella is a well known human pathogen that causes shigellosis. Four Shigella species are not valid taxa and are in fact groups within E. coli. The recent availability of fully-assembled Shigella genomes enabled the investigation of its genome rearrangement patterns. The study of genomic rearrangements in Shigella may further the understanding of pathogen bacteria evolution and selection on the architecture of their chromosomes.
This repository contains all data and scripts used in the project 'Genome evolution and pathoadaptation of Shigella'. Each directory corresponds to one of the three sections of the article.
This directory contains data, scripts and results corresponding to 1. Structure of the phylogenetic tree of E. coli and Shigella spp.
This directory contains data, scripts and results corresponding to 2. Accumulation of IS elements.
This directory contains data, scripts and results corresponding to 3. Rates of rearrangements.
This directory contains data, scripts and results corresponding to 4. Shigella-specific rearrangements.