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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.    Conclusion  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   .

Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences