title: Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.
abstract: BACKGROUND
  The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships.
  
  
  RESULTS
  We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a framework based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments.
  
  
  BACKGROUND
  Phylo-VISTA is available at http://www-gsd.lbl.gov/phylovista. It requires an Internet browser with Java Plug-in 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu
authors.affiliation: Center for Image Processing and Integrated Computing, Department of Computer Science, One Shields Avenue, University of California, Davis, CA 95616-8562, USA. phylovista@lbl.gov
authors.forename: Nameeta
authors.initials: N
authors.lastname: Shah
authors.forename: Olivier
authors.initials: O
authors.lastname: Couronne
authors.forename: Len A
authors.initials: LA
authors.lastname: Pennacchio
authors.forename: Michael
authors.initials: M
authors.lastname: Brudno
authors.forename: Serafim
authors.initials: S
authors.lastname: Batzoglou
authors.forename: E Wes
authors.initials: EW
authors.lastname: Bethel
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.forename: Bernd
authors.initials: B
authors.lastname: Hamann
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D003196:Computer Graphics; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007938:Leukemia / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface