title: Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences.
abstract: BACKGROUND
  When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences.
  
  
  RESULTS
  A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation.
  
  
  CONCLUSIONS
  With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL http://biocomp.iis.sinica.edu.tw/phylomlogo.
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan. arthur@iis.sinica.edu.tw <arthur@iis.sinica.edu.tw>
authors.forename: Arthur Chun-Chieh
authors.initials: AC
authors.lastname: Shih
authors.forename: D T
authors.initials: DT
authors.lastname: Lee
authors.forename: Chin-Lin
authors.initials: CL
authors.lastname: Peng
authors.forename: Yu-Wei
authors.initials: YW
authors.lastname: Wu
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D001717:Birds; D003626:Data Display; D018562:Disease Transmission, Infectious / Q000517:prevention & control; D020869:Gene Expression Profiling; D006388:Hemagglutinins / Q000235:genetics; D006801:Humans; D005585:Influenza in Birds / Q000235:genetics / Q000635:transmission; D008969:Molecular Sequence Data; D018035:Receptors, Odorant / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D012986:Software Validation; D014584:User-Computer Interface
chemical_list: D006388:Hemagglutinins; D018035:Receptors, Odorant