GenoPlast is no longer actively maintained.
Acquisition and loss of genetic material are essential forces in bacterial microevolution. They have been repeatedly linked with adaptation of lineages to new lifestyles, and in particular pathogenicity. GenoPlast implements a model-based method for using whole genome sequences to infer the patterns of genome content evolution. The method is described in Didelot, Darling and Falush (2009). A fundamental property of our model is that it allows the rates at which genetic elements are gained or lost to vary in time and from one lineage to another.
You may want to download the GenoPlast user guide in PDF format.
The paper describing the methods is also available: Didelot, Darling and Falush (2009)
If you have a question or a problem that is not discussed in the user guide, please get in touch.
The input matrix required by GenoPlast can be generated from a Mauve backbone file using the utility bbFilter which is available here for Linux32, Linux64, Mac and Windows.