Codon Usage Bias Simulation

Population Parameters

Population Size (N): 200

Mutation Rate: 0.001

×10⁻⁴

Selection Parameters

Selection Strength: 0.01

×10⁻³

Expression Level: High

Higher = stronger selection

Mutation Bias

GC → AT Bias: 1.0

×0.1 (1.0 = no bias)

tRNA Pool

tRNA Abundance Variation: High

Codon Usage Bias:
Synonymous codons aren't used equally. Optimal codons match abundant tRNAs, enabling faster and more accurate translation. Selection strength scales with gene expression level.

Codon Frequency Evolution

Optimal Codon

Sub-optimal Codons

tRNA Availability vs Codon Usage

Codon Adaptation Index (CAI) Over Time

Population Mean CAI

Equilibrium Prediction

Ribosome Speed Distribution

Fitness Landscape

Generation

Mean CAI
0.500

Optimal Codon %

50.0%

Translation Speed
1.00x

GC Content