The field of comparative genomics is currently in a period of accelerated development triggered by the recent explosion of genome sequencing (human, model organisms, bacteria, viruses, etc.) and the subsequent need to perform comparisons between two or more genomes. Comparative genomics tools can operate on either nucleic acid or protein sequence; some tools are specific to one while others can handle both. Most people think of alignment tools when discussing comparative genomics, but tools that determine common substrings are another important category. The whole-genome computational pipelines described in the Examples below were the first large-scale application of these techniques to pathogen diagnostic development. This took advantage of many of the tools described below and has clarified the need for many additional tools. Other tools that may have similar application to the design of microbial detection and forensic diagnostics are discussed in a recent survey paper.28
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