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

Arthur Chun-Chieh Shih1, DT Lee12*, Chin-Lin Peng2 and Yu-Wei Wu1

Author Affiliations

1 Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan

2 Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan

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BMC Bioinformatics 2007, 8:63  doi:10.1186/1471-2105-8-63

Published: 24 February 2007



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.


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.


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 webcite.