Generates plots of site-wise variation along a sequence alignment. SHiAT (Shannon Heterogeneity in Alignments Tool), it generates plots of site-wise variation along a sequence alignment (including the Shannon Entropy and Hamming Distance measures).
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.
Four measures are implemented:
- Shannon information entropy (by position)
- 1-(consensus frequency) (by position)
- 1-(heterozygosity index H) (by position)
- Hamming Distance (summed pairwise across alignment)

Requirements:
* Java

The license of this software is Free, you can free download and free use this calculator software.