Is there any software available for simulating a bacterial population which contains similar strains?
See these papers:

Assessing the reliability of eBURST using simulated populations with known ancestry

http://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-7-30

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670731/

SimBac: simulation of whole bacterial genomes with homologous recombination 

http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000044

Modeling Bacterial Population Growth from Stochastic Single-Cell Dynamics

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136116/

Also this one:

https://labs.wsu.edu/populationgenomics/resources/software-simulation-code/

There are many of them. The choice depends upon what exactly you need.