FLEA

FLEA (Full-Length Envelope Analyzer) is a tool for analyzing and visualizing long-read sequencing data. It is specially tailored for challenging sequences like the HIV env gene. It offers an end-to-end solution, from processing raw FASTQ reads to producing high-quality consensus sequences and insightful visualizations.

Key Features and Functionalities:

- Data Processing: FLEA processes FASTQ reads to generate high-quality consensus sequences, ensuring an accurate representation of viral populations.

- Alignment and Phylogenies: It constructs a codon-aware multiple sequence alignment from the consensus sequences and uses this alignment to infer phylogenetic relationships and evolutionary dynamics.

- Selection Pressure Analysis: FLEA analyzes gene-wide selective pressures, providing insights into the evolutionary pressures acting on the viral population over time.

- Interactive Visualizations: The tool includes a web application that offers interactive plots and visualizations, such as an annotated viral alignment browser, time series plots of evolutionary dynamics, and a phylogenetic tree browser.