PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
BMC Bioinformatics
; 16: 155, 2015 May 13.
Article
em En
| MEDLINE
| ID: mdl-25968323
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.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 ).
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Filogenia
/
Polimorfismo Genético
/
Tuberculose
/
Gráficos por Computador
/
Software
/
Genoma Bacteriano
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Mycobacterium tuberculosis
Tipo de estudo:
Prognostic_studies
Idioma:
En
Ano de publicação:
2015
Tipo de documento:
Article