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All of the scripts and programs for this workflow are open-source and available online for free to ensure that individual researchers and small groups are able to access and utilize the tools necessary to complete the workflow. In general, many available bioinformatic tools are free and open source, but the installation, operation and maintenance of these programs is often complex, requiring specific technical expertise or extensive detailed instructions and best practices in the field remain undefined.  It should also Sequencing, sharing, and publishing a genome sequence can certainly  be noted considered as an important process in its own right. Once a genome is shared other people can use  that genome for various and diverse purposes. However, just because one can stop after publishing and releasing  asequenced  genome sequence that does not mean one should ignore what one can do with the data. A genome sequence  is simply also  a starting place point  for analysis. Analysis of the genome in detail, many computational and laboratory analyses that can provide insight into evolution, ecology, physiology, biochemistry, metabolism,  and comparative genomics more. Such analyses  are both outside beyond  the scope of this workflow. These additional steps could include analyses such as aligning the genome to a close relative to look for rearrangements (e.g. Progressive Mauve REF), phylogenomic analysis (e.g. what?), looking for evidence of horizontal gene transfer (e.g. how?), looking for novel functions within the lineage (how?), examining genomic context (e.g. JContextExplorer, REF) workflow  and phylogenomic profiling (REF). MORE STUFF HERE. paper but that should not be taken as implying they are not interesting, useful or important.