This program performs Shannon entropy and median mobility shift (MMS) calculations for heteroduplex assays. Input should be in the same form as the HDent sample input file. The program reads the file and stores all the scans it finds there. Each scan is recorded as a list of (pixel number, intensity) pairs. The program normalizes this list so the total intensity is 1.0, then regards the result as a probability distribution and computes two statistics: median: the place in the lane which divides the scan's total signal in half. If, for example, the lane has one broad band in it, the median will fall somewhere in the middle of the band. entropy: a measure of the breadth of the distribution; this number is large for lanes with numerous smeared, overlapping bands and small for lanes with a few small, tight bands. These statistics were first used to analyze data from a heteroduplex mobility assay in a paper of Delwart et al., J. Virology 71:7498-7508, 1997. Medline The approach was developed to provide a quantitative measure of the intrapatient genetic diversification of HIV based on HMA and HTA experiments over the course of a single infection. High rates of diversification were correlated with long term survival. ***IMPORTANT: When comparing results of different gel scans, make sure you specify the same number of pixels for each analysis (which must be less than or equal to the lowest resolution of all the scans). Acknowledgements: This program is the work of many people: Bette Korber, David Wolpert, Avidan Neumann, Eric Delwart and Jim Mullins developed the original version applied in Delwart et al.; James Theiler wrote opt-3.5, the package used to handle command line arguments and Mark Muldoon wrote the code you are reading. This website was created by Satish Pillai. Click here for a detailed explanation of program output.