title: PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
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 ) 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.
  
  
  CONCLUSIONS
  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 ).
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK. ernest.diezbenavente@lshtm.ac.uk.|Engineering Sciences Division, School of Engineering, Cranfield University, Cranfield, UK. ernest.diezbenavente@lshtm.ac.uk.
authors.forename: Ernest D
authors.initials: ED
authors.lastname: Benavente
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK. francesc.coll@lshtm.ac.uk.
authors.forename: Francesc
authors.initials: F
authors.lastname: Coll
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK. nick.furnham@lshtm.ac.uk.
authors.forename: Nick
authors.initials: N
authors.lastname: Furnham
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK. ruth.mcnerney@lshtm.ac.uk.
authors.forename: Ruth
authors.initials: R
authors.lastname: McNerney
authors.affiliation: Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel St, London, UK. judith.glynn@lshtm.ac.uk.
authors.forename: Judith R
authors.initials: JR
authors.lastname: Glynn
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. sc11@sanger.ac.uk.
authors.forename: Susana
authors.initials: S
authors.lastname: Campino
authors.affiliation: Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia. arnab.pain@kaust.edu.sa.
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
authors.affiliation: Engineering Sciences Division, School of Engineering, Cranfield University, Cranfield, UK. f.mohareb@cranfield.ac.uk.
authors.forename: Fady R
authors.initials: FR
authors.lastname: Mohareb
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK. taane.clark@lshtm.ac.uk.|Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel St, London, UK. taane.clark@lshtm.ac.uk.
authors.forename: Taane G
authors.initials: TG
authors.lastname: Clark
mesh_terms: D003196:Computer Graphics; D016680:Genome, Bacterial; D005843:Geography; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic / Q000235:genetics*; D012984:Software; D014376:Tuberculosis / Q000235:genetics* / Q000382:microbiology