CheckAlign 2.0 computes two variations of the Shannon algorithm.
The tool computes the canonical algorithm introduced by Schneider and
Stephens in previous logos methodologies approaches for constructing
sequence logos from the input of gapped and ungapped protein and DNA
multiple alignments. The resulting logos represent each column of a
sequence alignment as a stack of letters of variable color and height
depending on the amino acid or nucleotide chemical nature and frequency.
CheckAlign 2.0 also focuses on other aspects of information theory
focusing concerning the diversity of species in an ecological community.
In this case, the tool provides accounts of both the abundance and
evenness of the species present in a community sample, by computing the
Shannon-Weaver diversity index (H) and the Equitability (EH) of these
CheckAlign 2.0 is distributed as a standalone software adapted to the
most common operating systems or as an online server accessible at the
Gypsy Database of Mobile Genetic Elements.