PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

Ernest D Benavente, Francesc Coll, Nick Furnham, Ruth McNerney, Judith R. Glynn, Susana Campino, Arnab Pain, Fady R Mohareb, Taane G. Clark

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Background 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. Results We have developed a web-based tool called PhyTB (http://pathogenseq.lshtm.ac.uk/phytblive/index.php webcite) 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. Conclusion 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 webcite).
Original languageEnglish (US)
JournalBMC Bioinformatics
Volume16
Issue number1
DOIs
StatePublished - May 13 2015

Fingerprint

Dive into the research topics of 'PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis'. Together they form a unique fingerprint.

Cite this