FLEA: the Full-Length Envelope Analyzer
FLEA (currently under heavy development) is the computational arm of the UCSD/Pacific Biosciences full length HIV-1 envelope sequencing protocol. It bridges the crevasse between raw reads and interpretable results, specializing in longitudinal samples and within-host evolution. There are 4 vizualizations:
Displays aggregated evolutionary metrics over time. These can be computed from the entire gp160, or from particular subregions.
Vizualizes site-level evolutionary metrics on an interactive 3D Env trimer structure, as well as a linear representation of the gene over time.
Provides a condensed view of the alignment, as well as a vizualization of residue kinetics over time, allowing the user to select combinations of sites of interest.
Displays an interactive phylogeny inferred from the sequences, including ancestral reconstructions showing where residue substitutions likely occured.
If you're already familiar, skip straight to the demo
, or continue scrolling for some pointers on how to explore your sequence data with FLEA