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

BMC Bioinformatics

Software

Arnab Pain¹  Fady R Mohareb²  Judith R Glynn³  Francesc Coll⁴  Ruth McNerney⁴  Nick Furnham⁴  Ernest D Benavente⁵  Taane G Clark⁶  Susana Campino⁷ 

[1] Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia;Engineering Sciences Division, School of Engineering, Cranfield University, Cranfield, UK;Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel St, London, UK;Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK;Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK;Engineering Sciences Division, School of Engineering, Cranfield University, Cranfield, UK;Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK;Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel St, London, UK;Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK;

关键词: Tuberculosis;    Phylogeny;    Sequencing;   

DOI  :  10.1186/s12859-015-0603-3

 received in 2015-01-14, accepted in 2015-04-29,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundPhylogenetic-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.ResultsWe 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.ConclusionPhyTB 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).

【 授权许可】

CC BY   
© Benavente et al.; licensee BioMed Central. 2015