VirtualMicrobes 0.2.5

Virtual Microbe Evolutionary Simulator

README

Virtual Microbes Evolutionary Simulator

Features

• Individual based model of evolving microbes.

• Explicit model of evolving genome.

• Spatially extended environment.

• Microbes evolve metabolic capacities to exploit environmental nutrients.

Dependencies and scripts

• depends on:

  • cython

  • matplotlib

  • networkx (network analysis and drawing)

  • ete3 (tree drawing and phylogenetics)

  • others see requirements.txt

Install

pip install VirtualMicrobes

Usage

can’t wait to simulate:

vermicelli.py evo <simulation_dir>

open pandora’s box of options:

• vermicelli.py --help

• vermicelli.py evo --help

Documentation

http://virtualmicrobes.readthedocs.io/en/latest/ (in progress..) CHANGELOG ———

nothing changed here