PHYLOViZ

PHYLOViZ integrates and visualizes phylogenetic and sequence-based typing data to support microbial epidemiology and analysis of bacterial strain relatedness from High Throughput Sequencing (HTS) datasets.

Key Features:

• Data Integration: Integrates sequence-based typing methods and profiles across multiple typing databases to enable standardized comparison of strains and clones.
• Visualization Capabilities: Provides scalable visualization of phylogenetic patterns within large datasets to reveal genetic relationships among microbial taxa.
• Efficient Distance Computation: Implements an average-case linear-time algorithm to compute pairwise Hamming distances among a set of taxa under a specified threshold.
• Algorithmic Integration and Speed: Integrates the linear-time Hamming distance algorithm into established phylogenetic inference methods to accelerate querying of local phylogenetic patterns within extensive typing databases.

Scientific Applications:

• Microbial Epidemiology: Enables analysis of bacterial strain relatedness for epidemiological surveillance and outbreak investigation using HTS-derived data.
• Pathogen Evolution: Supports studying pathogen evolution and population structure by revealing genetic relationships among isolates.
• Typing Database Analysis: Facilitates rapid querying and comparison of profiles within extensive typing databases to support common nomenclatures for strains or clones.

Methodology:

Computational methods include an average-case linear-time algorithm for pairwise Hamming distance computation under a specified threshold, theoretical analysis and extensive experimental validation of the algorithm, and integration with phylogenetic inference methods.