Lawrence Berkeley National Laboratory

Motivation. The power of multi-sequence comparison for biological discovery is well established and sequence data from a growing list of organisms is becoming available. Thus, a need exists for computational strategies to visually compare multiple aligned sequences to support conservation analysis across various species. To be efficient these visualization algorithms require the ability to universally handle a wide range of evolutionary distances while taking into account phylogeny Results. We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing the similarity of DNA sequences among multiple species while considering their phylogenic relationships. Features include a broad spectrum of resolution parameters for examining the alignment and the ability to easily compare any subtree of sequences within a complete alignment dataset. Phylo-VISTA uses VISTA concepts that have been successfully applied previously to a wide range of comparative genomics data analysis problems. Availability Phylo-VISTA is an interactive java applet available for downloading at http://graphics.cs.ucdavis.edu/~;nyshah/Phylo-VISTA. It is also available on-line at http://www-gsd.lbl.gov/phylovista and is integrated with the global alignment program LAGAN at http://lagan.stanford.edu.Contactphylovista@lbl.gov