Molecular dynamics (MD) simulation and its analysis is one of the key tools to provide deeper insights into biological systems at the molecular level, and the results from MD simulation often make critical impacts on defining in-silico models for biological phenomena and validating hypothesis. Recent advances in computing resources and MD simulators significantly accelerate the MD simulation time and thus increase the amount of trajectory data. However, analyzing MD trajectories is still time consuming and often a difficult task even though many laboratories routinely perform MD simulations. ST-analyzer, http://im.bioinformatics.ku.edu/st-analyzer, is a standalone GUI toolset to perform various trajectory analyses with commonly used built-in analysis modules. ST-analyzer has several outstanding features compared to other existing analysis tools: i) handling various formats of trajectory files from CHARMM, NAMD, GROMACS, and Amber, ii) intuitive web-based GUI environment - minimizing administrative load and reducing users' burdens from adapting new software environments, iii) platform independent design scheme - works with any existing OS, iv) easily integrates into job queuing systems - providing options of batch processing either on the cluster or in interactive mode, and v) providing independence between foreground GUI and background modules - makes it easier to add personal modules or to recycle/integrate pre-existing scripts utilizing other analysis tools. The current ST-analyzer contains nine main modules and 18 sub-processors including density profile, lipid deuterium order parameters, lipid surface area, lipid hydrophobic thickness, and more.