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.


Loading loading...
Search View Mode VCF Analysis
Search Type: Search by: Enter your term:
loading...
Legend
Psst! Click in the Show button to show the tool bar
No collapsing searches performed
Legend

Lineage1

Lineage1.1

Lineage1.1.1

Lineage1.1.1.1

Lineage1.1.2

Lineage1.1.3

Lineage1.2

Lineage1.2.1

Lineage1.2.2

Lineage2

Lineage2.1

Lineage2.2

Lineage2.2.1

Lineage2.2.1.1

Lineage2.2.1.2

Lineage2.2.2

Lineage3

Lineage3.1

Lineage3.1.1

Lineage3.1.2

Lineage3.1.2.1

Lineage3.1.2.2

Lineage4

Lineage4.1

Lineage4.1.1

Lineage4.1.1.1

Lineage4.1.1.2

Lineage4.1.1.3

Lineage4.1.2

Lineage4.1.2.1

Lineage4.2

Lineage4.2.1

Lineage4.2.2

Lineage4.2.2.1

Lineage4.3

Lineage4.3.1

Lineage4.3.2

Lineage4.3.2.1

Lineage4.3.3

Lineage4.3.4

Lineage4.3.4.1

Lineage4.3.4.2

Lineage4.3.4.2.1

Lineage4.4

Lineage4.4.1

Lineage4.4.1.1

Lineage4.4.1.2

Lineage4.4.2

Lineage4.5

Lineage4.6

Lineage4.6.1

Lineage4.6.1.1

Lineage4.6.1.2

Lineage4.6.2

Lineage4.6.2.1

Lineage4.6.2.2

Lineage4.7

Lineage4.8

Lineage4.9

Lineage5

Lineage6

Lineage7

LineageBOV

LineageBOV_AFRI

More about lineages