References
==============

.. [Barrick2009a] Barrick et al. (2009) Genome evolution and adaptation in a long-term experiment with *Escherichia coli*. *Nature* **461**:1243-1247.
.. [Barrick2009b] Barrick, J.E., Lenski, R.E. (2009) Genome-wide mutational diversity in an evolving population of *Escherichia coli*. *Cold Spring Harb. Symp. Quant. Biol.* **74**:119-129.  
.. [Blount2008] Blount e al. (2008) Historical contingency and the evolution of a key innovation in an experimental population of *Escherichia coli*. *Proc. Natl. Acad. Sci. U.S.A.* **105**:7899–7906.
.. [Blount2011] Barrick, J.E., Lenski, R.E. (2009) Genome-wide mutational diversity in an evolving population of *Escherichia coli*. *Cold Spring Harb. Symp. Quant. Biol.* **74**:119-129.  
.. [McKenna2010]  McKenna et al. (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. *Genome Research*  **20**:1297-1303.
.. [Deatherage2014]  Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using *breseq*. *Methods Mol. Biol.* **1151**: 165–188.
.. [Barrick2014]  Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C., Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G.(2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using *breseq*. *BMC Genomics* **15**:1039.
.. [Deatherage2015]  Deatherage, D.E., Traverse, C.C., Wolf, L.N., Barrick, J.E. (2015) Detecting rare structural variation in evolving microbial populations from new sequence junctions using *breseq*. *Front. Genet.* **5**:468.