Humphreys I, Fleming V, Fabris P, Parker J, Schulenberg B, Brown A, Demetriou C, Gaudieri S, Pfafferott K, Lucas M, Collier J, Huang KH, Pybus OG, Klenerman P, Barnes E (2009) Full-length characterisation of the hepatitis C virus subtype 3a reveals novel hypervariable regions under positive selection during acute infection. Journal of Virology 83:11456-66

Author: Joe Parker

Latest version: 1.1

Download program and documentation (MAC) (PC, UNIX, LINUX)

Download manual (pdf)


SHiAT = Shannon Heterogeneity in Alignments Tool

This application provides an intuitive graphical interface for the simultaneous calculation of three measures of site-wise variation in DNA or RNA alignments. The Shannon Information index, Hamming distance and (1-consensus frequency) are all calculated and displayed in a series of graphical plots. Multiple alignments may be imported and compared, and a data view panel allows easy copy-and-pasting into external applications.

This package is available as a Java application (jarfile) that can be easily run on most types of computer. See the manual for more details.


To run SHiAT on Mac OS, simply double-click the application icon. To run SHiAT on other computers, run the executable jarfile. This requires that your computer has Java 1.5.0 (J2SE 5.0) or higher installed; see included documentation for details.