Aegis User Guide

A walkthrough of how to read Aegis analysis results. Each section maps to one layer of the UI — summary header, genome browser, and global surveillance — plus worked examples.

Read this first

Viral genomes typically score 60–75% on the AI Anomaly Score even on reference FASTAs. This reflects training-data bias, not a danger signal. See Genome browser for details.

Sections

11 · Watching progress
12 · History & export
13 · API keys
14 · MCP setup
20 · Overview
21 · Summary header
22 · Genome browser
23 · Global surveillance
24 · Worked examples

Three result layers

Summary header — risk score, BSL, pathogen/AMR/virulence/chimera fields.
Genome browser — ORFs, DIAMOND protein hits, BLAST taxonomy, low-complexity regions, AI anomaly tracks (150 bp / 2 kb / 8 kb).
Global surveillance — environment/biome Sankey, bubble map, divergence distribution (Select Agents only).