ViPR: an open bioinformatics database and analysis resource for virology research

Pickett, Brett E.; Sadat, Eva L.; Zhang, Yun; Noronha, Jyothi M.; Squires, R. Burke; Hunt, Victoria; Liu, Mengya; Kumar, Sanjeev; Zaremba, Sam; Gu, Zhiping; Zhou, Liwei; Larson, Christopher N.; Dietrich, Jonathan; Klem, Edward B.; Scheuermann, Richard H.

Once complete, the Archaeopteryx phylogenetic tree viewer can be used to quickly visualize, explore and manipulate the resulting tree using typical actions such as re-rooting, select subtrees, branch swapping, etc. This application has recently been customized to take advantage of the extensive sequence metadata within the ViPR database by allowing user-driven coloring of tree 'leaves' according to year, country of isolation or host from which the strain was originally isolated. The customized graphic can then be exported for enhanced interpretation and inclusion in publications. For the current use case, the phylogeny was calculated for all sequences matching our initial query and colored by the country of isolation. This tree reconstruction shows the major branching structures that separate sequences primarily according to serotype ( Figure 1A) . However, within the serotype 2 branch, two separate US lineages can be identified-one corresponding to a Brazilian lineage and one corresponding to a Nicaraguan lineage-suggesting that two different serotype 2 introduction events have occurred in the United States.