PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis
AuthorsBenavente, Ernest D
Glynn, Judith R.
Mohareb, Fady R
Clark, Taane G.
Permanent link to this recordhttp://hdl.handle.net/10754/552987
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AbstractBackground 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).
CitationPhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis 2015, 16 (1) BMC Bioinformatics
PubMed Central IDPMC4429496
- PolyTB: a genomic variation map for Mycobacterium tuberculosis.
- Authors: Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, Viveiros M, Portugal I, Drobniewski F, Gagneux S, Glynn JR, Pain A, Parkhill J, McNerney R, Martin N, Clark TG
- Issue date: 2014 May
- The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country.
- Authors: Cardoso Oelemann M, Gomes HM, Willery E, Possuelo L, Batista Lima KV, Allix-Béguec C, Locht C, Goguet de la Salmonière YO, Gutierrez MC, Suffys P, Supply P
- Issue date: 2011 Mar 25
- [Future prospects of molecular epidemiology in tuberculosis].
- Authors: Matsumoto T, Iwamoto T
- Issue date: 2009 Dec
- SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
- Authors: Coll F, Mallard K, Preston MD, Bentley S, Parkhill J, McNerney R, Martin N, Clark TG
- Issue date: 2012 Nov 15
- Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis.
- Authors: Alland D, Lacher DW, Hazbón MH, Motiwala AS, Qi W, Fleischmann RD, Whittam TS
- Issue date: 2007 Jan