Humphreys I, Fleming V, Fabris P, Parker J, Schulenberg B, Brown A, Demetriou C, Guadieri 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 In press

Author: Joe Parker

Latest version: 1.1

Download program and documentation (MAC OS) (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 sitewise 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.