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

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, PhylomLogo 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, Phy...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Arthur Chun-Chieh Shih, D. T. Lee, Chin-Lin Peng, Yu-Wei Wu
• Keywords: BMCBI 2007, Epidemic Virus Sequences, Sequences, Virus Sequences