Configuration and command reference

==Main Configuration Files==

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

==Analyze Mode==

• Guidelines to Analyze Mode
• 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