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:

Evolutionary trajectory

Displays aggregated evolutionary metrics over time. These can be computed from the entire gp160, or from particular subregions.

Gene-wide information

Vizualizes site-level evolutionary metrics on an interactive 3D Env trimer structure, as well as a linear representation of the gene over time.

Amino-acid sequences

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.

Inferred phylogenies

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.
Please visit our live demo and explore. Email us any queries about the sequencing protocol or analysis pipeline.
Ben Murrell, Kemal Eren, Steven Weaver, and Sergei Kosakovsky Pond