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    Software: Adaptively aggregated trees with sampling-based subscale representation
    Submitted by Dr. Leonid Zaslavsky; posted on Wednesday, May 21, 2008

    Submitter

    METHODOLOGY ARTICLE:
    Leonid Zaslavsky, Yiming Bao and Tatiana A. Tatusova. 2008. ``Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation''. BMC Bioinformatics 9:237. www.biomedcentral.com/1471-2105/9/237

    BACKGROUND

    With the amount of influenza genome sequence data growing rapidly, researchers need machine assistance in selecting datasets and exploring the data. Enhanced visualization tools are required to represent results of the exploratory analysis on the web in an easy-to-comprehend form and to facilitate convenient information retrieval.

    RESULTS

    We developed an approach to visualize large phylogenetic trees in an aggregated form with a special representation of sub-scale details. The initial aggregated tree representation is built with a level of resolution automatically selected to fit into the available screen space, with terminal groups selected based on sequence similarity. The default aggregated representation can be refined by users interactively. Structure and data variability within terminal groups are displayed using small trees that have the same vertical size as the text annotation of the group. These subscale representations are calculated using systematic sampling from the corresponding terminal group. The aggregated tree containing terminal groups can be annotated using aggregation of structured metadata, such as seasonal distribution, geographic locations, etc.

    AVAILABILITY

    The algorithms are implemented in JavaScript within the NCBI Influenza Virus Resource.

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