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stochastic simulation of gene expression with site-specific translation rates

Project description



Build Status Documentation Status

A flexible gene expression simulator with codon-specific translation rates.


Pinetree requires Python, CMake, and a modern C++ compiler. Python 3 is recommended.


To install the latest stable version of pinetree from PyPI, run the following:

pip3 install cmake  # CMake must be installed before installing pinetree
pip3 install pinetree 

The latest development build may be installed from GitHub as follows:

pip3 install cmake   
git clone
cd pinetree
pip3 install .


Full documentation is available here.

You may also build the documentation from the source code. Building the documentation requires sphinx.

pinetree/ build_sphinx

Reproducing plots from manuscript

This repository contains scripts to reproduce the simulations and plots from the manuscript that describes Pinetree. R and the R packages cowplot, readr, dplyr, and stringr are required to generate plots. Run the following to reproduce the plots from the manuscript:

python3 ./examples/
python3 ./examples/
Rscript plots.R

To simulate a bacteriophage T7 infection, run the following script.

# WARNING: This simulation takes approximately 2-3 hours to complete
python3 ./examples/

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pinetree-0.4.0.tar.gz (548.8 kB view hashes)

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