PhyTB

PhyTB enables phylogenetic analysis and visualization of Mycobacterium tuberculosis genomes to identify clade-informative polymorphisms and relate genomic variation to geographic and epidemiological context.

Key Features:

• Phylogenetic Tree Visualization: Visualizes phylogenetic trees to explore intra- and inter-strain diversity in Mycobacterium tuberculosis.
• Sample Positioning (VCF): Accepts Variant Call Format (VCF) files to determine sample placement within the phylogeny and identify clade-informative polymorphisms.
• Geographical Mapping: Summarizes the geographical distribution of alleles and strain types to correlate genetic variation with spatial epidemiological data.
• Clade-Informative Polymorphism Identification: Identifies clade-informative polymorphisms within M. tuberculosis genomes to aid strain classification and lineage inference.
• Integration with Epidemiological Data: Contextualizes genomic variation with epidemiological data to relate genetic differences to transmission dynamics.
• Extensibility for Other Organisms: Can be adapted to phylogenetic studies of other organisms via modification of the source code.

Scientific Applications:

• Strain Classification: Supports classification and molecular barcoding of M. tuberculosis strains using phylogenetic placement and clade-informative polymorphisms.
• Outbreak Investigation: Supports investigation of disease outbreaks and transmission pathways by combining phylogenetic relationships with geographic distribution data.
• Genotype-Phenotype Associations: Enables assessment of associations between genetic variants and phenotypic traits, including drug-resistance profiles, when phenotypic data are available.

Methodology:

Uses whole genome sequencing data to construct phylogenetic trees and identify genomic variations; accepts VCF files for sample placement; combines genetic information with geographical mapping.