Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in tuberculosis pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance [1,2]. Some modern strains (e.g. Beijing, Euro-American, Haarlem) are believed to exhibit more virulent phenotypes compared to ancient ones (e.g. East African, Indian, M. africanum) . M. tuberculosis is relatively clonal, with little recombination and a low mutation rate . Like other bacterial genomic settings, the construction of phylogenetic trees using sequence data facilitates taxonomic localisation and the evolutionary analysis. The growing availability of M. tuberculosis whole genome sequences is leading to the full characterisation of single nucleotide polymorphisms (SNPs) and other nucleotide variation, such as insertions and deletions (indels). A SNP–based barcode has been developed to discriminate strain-types . Trees constructed using genome-wide variation have greater discriminatory power than traditional genotyping approaches such as MIRU-VNTR and spoligotyping . Clades reflecting strain type variations may be used to investigate disease outbreaks or transmission events, where samples are identified through apparent identical genomic signatures [5,6]. The tree also provides a structure to identify variants that can be used to investigate clinically important traits such as drug resistance . The primary mechanism for acquiring resistance is the accumulation of point mutations in genes coding for drug-targets or -converting enzymes (e.g. katG, inhA, rpoB, pncA, embB, rrs, gyrA, gyrB genes) , and these mutations may exist in multiple lineages in the tree, reflecting homoplasy events. Some mutations thought to be related to drug resistance are actually not, but instead strain-informative . With the increased application of sequencing technologies within clinical and microbiological research settings, it is important that informatic tools are available to identify informative strain-type and drug resistance related variants. Web-browsers for the visualisation of M. tuberculosis genomic variation exist [8-10], but there is limited connectivity with phylogenetic trees and downstream analysis, especially involving strain-types and drug resistance. In addition, there is little provision for uploading new data, such as standard variant call files (VCFs) (www.htslib.org). Here we present the PhyTB tool, which facilitates the phylogenetic exploration of M. tuberculosis isolates, including the display of clade-specific informative and drug resistance markers and their genomic annotation. Using the browser, it is possible to upload multiple standard genomic variant call files (VCF format) to identify the closest relative within the M. tuberculosis complex global phylogeny, thereby potentially assisting their interpretation in a clinical or epidemiological context. Source code is available to facilitate the development of sites for other organisms with genomes that can be represented in a phylogeny.