PhyloTrack

PhyloTrack performs phylogenetic analysis and visualization of bacterial genomes, focusing on Mycobacterium tuberculosis, to map genomic variation and support evolutionary and epidemiological investigations.

Key Features:

• Phylogenetic Tree Visualization: Interactive visualization of phylogenetic trees for detailed examination of evolutionary relationships and intra- and inter-strain diversity in M. tuberculosis.
• Variant Analysis (VCF): Support for Variant Call Format (VCF) uploads to determine sample positions within phylogenies and identify clade-informative polymorphisms.
• Geographical Mapping: Map-based summaries of geographical distribution of alleles and strain types to contextualize genomic variation in epidemiological settings.
• Data Integration: Incorporation of large variants and phenotypic data, including drug-resistance profiles, to evaluate genotype–phenotype associations.
• Genome Browser Integration: Locus-level inspection via integrated genome browser capabilities for detailed sequence context analysis.
• Customizability: Extensible analysis capability to adapt phylogenetic and variant workflows to organisms beyond M. tuberculosis.

Scientific Applications:

• Evolutionary analysis: Testing evolutionary hypotheses and characterizing strain relationships and diversity.
• Outbreak and transmission investigation: Tracing disease outbreaks and transmission events through phylogenetic placement of samples.
• Classification and molecular barcoding: Supporting classification of strains and identification of molecular barcodes and clade-defining markers.
• Public health genomics: Integrating genomic, epidemiological, and geographical data for surveillance and microbial genomics studies.

Methodology:

Operates on whole genome sequencing data, accepts VCF file uploads for variant mapping to tree positions, employs JavaScript and the D3.js library for dynamic visualization, and integrates JBrowse for genome browsing.