Using Stand Alone VISTA

In addition to using VISTA through the web server portal, one can also download the visualization module as a stand-alone Java program to create alignment visualization and perform conservation analysis locally. The program is available free for academic and nonprofit research and for a licensing fee to commercial entities. The alignment programs, such as AVID or LAGAN, can be downloaded separately under similar conditions. A detailed Readme file accompanies the package.

The input to stand-alone VISTA consists of one or more alignment files, a "plotfile" that contains parameters for running VISTA, and several optional annotation files (gene annotation, single-nucleotide polymorphisms, repeats, and so on). The stand-alone VISTA is highly customizable, and provides the user with a variety of options for visualization and output. Although the sheer number of options described in the documentation for the stand-alone version of the program can intimidate the user, it is important to note that almost all these parameters are optional. It is possible to get acceptable output with just the following bare-bones plotfile:

COORDINATE human ALIGN alignment.out

SEQUENCES human mouse END

The stand-alone version of the VISTA program provides certain features that are not available through the online tools described earlier, such as a "DIFFS" mode, in which the plot represents percent difference, not percent identity— useful for analyzing closely related species. On the other hand, it also only provides static output and does not show any of the precomputed whole-genome alignments available through the VISTA Browser. Researchers are encouraged to take these differences into account when choosing the appropriate tool for a particular task.

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