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..)