Created by Ernest Diez Benavente
To illustrate the usefulness of the PhyloTrack library we have created PhyTB, an application for the interactive study of variation in M.tuberculosis where 1601 whole-genome sequences of Mycobacterium tuberculosis complex
isolates (See ENA Study Accession Numbers) (the etiological agent of tuberculosis) from different areas
of the world and with representation of all seven major lineages
and sub-lineages in which 91k SNPs have been identified comparing to the H37Rv reference [GenBank:NC_000962.3]. Mtb is relatively clonal, with little recombination,
and variant-based analyses typically involve the construction
of phylogenetic trees, demonstrating clustering within 7 main
lineages and sub-lineages. Lineage-specific differences in the
virulence of clinical isolates have been reported across independent
experimental systems with modern lineages, such as Beijing
and Euro-American Haarlem strains believed to exhibit more
virulent phenotypes compared to ancient lineages, such as East
African, Indian and M. africanum strains.
In order to show the functionality of the tool, we deployed four examples to reflect different scenarios that users can find interesting.
NOTE: In order to browse the specific samples of another Lineage or Country as in the examples provided, the "Browse the whole Phylogenetic Tree" option should be selected, then in the tool bar:
- Select the "Collapsing Search" at the "Search Type" field.
- Select the attribute that is going to be used (Lineage, Country, etc) at the "Search by" field.
- Insert your search term using the drop-down list.
No collapsing searches performed