Ambiscript Mosaic is an Adobe Flash®-based application that uses a color-coded ambigraphic nucleic acid notation to reveal the prevalence of nucleotide polymorphisms in multiple sequence alignments1.  The open source application is available for download or use online.  The source code for the alignment tool can be found on Google Code.

Rozak DA, Rozak AJ. 2014. Using a color-coded ambigraphic nucleic acid notation to visualize conserved palindromic motifs within and across genomes. BMC Genomics 15:52. (PMID: 24447494)