Features of CHECKALIGN 2.0

CheckAlign generates graphical representations of DNA or protein multiple alignments sequences, creating outputs in two formats: PDF and PostScript.


The update of CheckAlign 2.0 adapts the logo maker to the most common operating systems updates and additionally focused on an implementation of the Shannon-Weaver algorithm to characterize species diversity in a community.



Logo obtained using Shannon’s algorithm with standard deviation bars.

Estimating diversity index measures for one or more biological or molecular samples.




Users may build the logo from a gapped alignment considering the gap as another nucleotide or amino acid species; moreover they can use the correction factor (recommended for small alignments) and depict standard deviation bars. Note that the “frequency algorithm” option creates a logo but the representation results in an overestimation of the true consensus.