Pinetree – a flexible gene expression simulator with codon-specific translation rates


Pinetree is a stochastic gene expression simulator that tracks polymerases and ribosomes at the single-molecule level. It includes nucleotide-resolution transcription and translation rates. This granularity allows users to simulate the effects of codon-usage bias and dinucleotide bias on gene expression.

Pinetree is a stochastic simulation that is implemented in Python with a C++ back-end and designed to be highly efficient. On a desktop-class CPU, simulating gene expression in a 40 kilobase viral genome for 30 minutes takes about 3 hours of computation time.

Developer Documentation

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