BackgroundududPhylogenetic-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.udResultsududWe 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.udConclusionududPhyTB 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).
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机译:背景,结核分枝杆菌和其他细菌基因组的基于进化论分类是研究进化假设,疾病暴发和传播事件的核心分析。全基因组测序正在提供对菌株内和菌株间多样性潜在的基因组变异的新见解,从而有助于细菌的分类和分子条形码。应变研究的障碍之一是缺乏用户交互解决方案来询问和可视化系统发育树设置中的变异。 udResults ud ud我们已经开发了一种基于网络的工具PhyTB(http://pathogenseq.lshtm.ac。 uk / phytblive / index.php网站),以帮助系统发育树可视化和鉴定结核分枝杆菌进化枝信息性多态性。可以上传变量调用格式文件以确定树中的示例位置。地图视图总结了等位基因和菌株类型的地理分布。 PhyTB的实用性在来自1,601个结核分枝杆菌分离株的序列数据中得到了证明。 udConclusion ud udPhyTB结合了结核分枝杆菌在流行病学,地理和系统发育背景下的基因组变异。通过合并较大的变体和表型数据(例如耐药性谱)以及评估基因型与表型的关联性,可以进一步利用工具。可以使用源代码来为其他生物开发类似的网站(http://sourceforge.net/projects/phylotrack网站)。
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