  Motivation: Gene blocks are genes co-located on the chromosome. In many
cases, genes blocks are conserved between bacterial species, sometimes as
operons, when genes are co-transcribed. The conservation is rarely absolute:
gene loss, gain, duplication, block splitting, and block fusion are frequently
observed. An open question in bacterial molecular evolution is that of the
formation and breakup of gene blocks, for which several models have been
proposed. These models, however, are not generally applicable to all types of
gene blocks, and consequently cannot be used to broadly compare and study gene
block evolution. To address this problem we introduce an event-based method for
tracking gene block evolution in bacteria. Results: We show here that the
evolution of gene blocks in proteobacteria can be described by a small set of
events. Those include the insertion of genes into, or the splitting of genes
out of a gene block, gene loss, and gene duplication. We show how the
event-based method of gene block evolution allows us to determine the
evolutionary rate, and to trace the ancestral states of their formation. We
conclude that the event-based method can be used to help us understand the
formation of these important bacterial genomic structures. Availability: The
software is available under GPLv3 license on
http://github.com/reamdc1/gene_block_evolution.git Supplementary online
material: http://iddo-friedberg.net/operon-evolution Contact: Iddo Friedberg
<EMAIL_ADDRESS>