PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus ge

Background: Results of phylogenetic analysis are often visualized as phylogenetic trees. Such a tree can typically only include up to a few hundred sequences. When more than a few thousand sequences are to be included, analyzing the phylogenetic relationships among them becomes a challenging task. The recent frequent outbreaks of influenza A viruses have resulted in the rapid accumulation of corresponding genome sequences. Currently, there are more than 7500 influenza A virus genomes in the database. There are no efficient ways of representing this huge data set as a whole, thus preventing a further understanding of the diversity of the influenza A virus genome. Results: Here we present a new algorithm, “PhyloMap”, which combines ordination, vector quantization, and phylogenetic tree construction to give an elegant representation of a large sequence data set. The use of PhyloMap on influenza A virus genome sequences reveals the phylogenetic relationships of the internal genes that...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Jiajie Zhang, Amir Madany Mamlouk, Thomas Martinetz, Suhua Chang, Jing Wang 0003, Rolf Hilgenfeld
• Keywords: Biometrics, BMCBI 2011, Genome Sequences, Vector Quantization, Virus Genomes