avida-ed-library-build/docs/documentation/Configuration-and-command-reference.md

Main Configuration Files

• Avida.cfg
• Events File
• Environment File
• Instruction Set
• instset-heads.cfg
• default-heads.org
• Analyze File

Analyze Mode

• Analyze File
• Sample Analyze Programs

Subpopulations (Demes)

• Deme introduction
• Deme migration

Misc. Configuration

• Quirks
• Setting up Fixed-Length Organisms
• Introduction to Parasites
• Gradient Resources
• Internal resources
• Using mating types (separate sexes)
• Energy model configuration