Introduction

Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria. One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting.We have developed a web-based tool called PhyTB ( http://pathogenseq.lshtm.ac.uk/phytblive/index.php ) to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant Call Format files can be uploaded to determine a sample position within the tree. A map view summarises the geographical distribution of alleles and strain-types. The utility of the PhyTB is demonstrated on sequence data from 1,601 M. tuberculosis isolates.PhyTB contextualises M. tuberculosis genomic variation within epidemiological, geographical and phylogenic settings. Further tool utility is possible by incorporating large variants and phenotypic data (e.g. drug-resistance profiles), and an assessment of genotype-phenotype associations. Source code is available to develop similar websites for other organisms ( http://sourceforge.net/projects/phylotrack ).

Publications

  1. PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
    Cite this
    Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, Campino S, Pain A, Mohareb FR, Clark TG, 2015-05-01 - BMC bioinformatics

Credits

  1. Ernest D Benavente
    Developer

    Engineering Sciences Division, School of Engineering

  2. Francesc Coll
    Developer

    Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine

  3. Nick Furnham
    Developer

    Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine

  4. Ruth McNerney
    Developer

    Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine

  5. Judith R Glynn
    Developer

    Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine

  6. Susana Campino
    Developer

    Wellcome Trust Sanger Institute, Hinxton, Germany

  7. Arnab Pain
    Developer

    Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology

  8. Fady R Mohareb
    Developer

    Engineering Sciences Division, School of Engineering

  9. Taane G Clark
    Investigator

    Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine

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Summary
AccessionBT000239
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByTaane G Clark