Introduction

Bacteria, unlike us, can reproduce on their own. They do however have mechanisms that transfer DNA between organisms, a process more formally known as recombination. The mechanisms by which recombination takes place have been studied extensively in the laboratory but much remains to be understood concerning how, when and where recombination takes place within natural populations of bacteria and how it helps them to adapt to new environments. ClonalOrigin performs a comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.

ClonalOrigin is described in the following paper:

Didelot X, Lawson D, Darling A, Falush D (2010) Inference of homologous recombination in bacteria using whole genome sequences. Genetics doi:10.1534/genetics.110.120121 http://www.genetics.org/cgi/content/abstract/genetics.110.120121v1

Usage

Instructions for how to download and install ClonalOrigin are available at: http://code.google.com/p/clonalorigin/wiki/Download_And_Install_ClonalOrigin

Instructions for how to use ClonalOrigin once installed are available at: http://code.google.com/p/clonalorigin/wiki/FromGenomeAssemblyToRecombination