wgVISTA is a set of programs for comparing DNA sequences from two microbial species up to 10 megabases long and visualize these alignments with annotation information ( Frazer et al., 2004, Mayor et al., 2000).
It is implemented as an on-line server that provides access to the whole-genome alignment pipeline.
The alignment program behind the pipeline is Shuffle-LAGAN, a glocal alignment algorithm that is able to find rearrangements (inversions, transpositions and some duplications) in a global alignment framework (Brudno et al., 2003). The algorithm uses CHAOS local alignments to build a map of the rearrangements between the sequences, and LAGAN to align the regions of conserved synteny.
wgVISTA visualization module is the VISTA Browser, an interactive Java applet, which is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. The browser's clean display makes it easy to identify sequence similarities and differences.