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The ST-analyzer is a standalone graphical user interface toolset used to perform molecular dynamics (MD) simulation trajectory analyses. Its unique implementation scheme and intuitive user interfaces are designed to reduce the user's learning curve and maximize software flexibility. The embedded database and quick search engine help users maintain both submitted and ongoing jobs. In addition to validated built-in modules, the ST-analyzer supports a range of computing sources that include personal computers, community-wide cluster machines, multiple operating systems, and MD simulation programs. The ST-analyzer, presented by Jong Cheol Jeong et al. on page 957 (DOI: 10.1002/jcc.23584), can be freely downloaded from http://im.bioinformatics.ku.edu/ST-analyzer.