Vertical gene transmission and horizontal gene transfer

The most important information to look for is the regions of DNA that are present in one isolate and absent in the other. The core genomes should align with each other, with the exception of some sequence differences due to mutation. However, large losses in one isolate could be a sign of horizontal gene transfer. Therefore, clusters of changes or the presence of a block of DNA in one strand that is absent in the other would indicate horizontal gene transfer. It may also be helpful to identify the homologs of each gene in each isolate to see if the individual genes have been acquired or lost.