| Summary: | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>A multiple-logo alignment visualization tool, called <it>Phylo-mLogo</it>, is presented in this paper. <it>Phylo-mLogo </it>calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, <it>Phylo-mLogo </it>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, <it>Phylo-mLogo </it>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.</p> <p>Conclusion</p> <p>With <it>Phylo-mLogo</it>, 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 <it>Phylo-mLogo </it>can be found at URL <url>http://biocomp.iis.sinica.edu.tw/phylomlogo</url>.</p>
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