Coalescent Simulations

Simulates different coalescents

Dependencies

• Python 3.6
• Requirements:
  • biopython==1.68
  • matplotlib==2.0.0
  • numpy==1.12.0
  • scikit-learn==0.18.1
  • scipy==0.19.0

Usage

Parameters can be customized. For available options:

python main.py -h

1. Model Test

   python main.py --test
   

• Produces a single tree for Kingman and Bolthausen-Sznitman
• Enable graphics output with --graphics
• Current default setting:
  • Sample Size: 10
  • Mutation Rate: 0.9
  • Number of Iterations: 300

2. Experiment

• Executes a number of Experiments and records experimental data for analysis
• Current default setting:
  • Sample Size Range: (5, 10, 5)
  • Init Mutation Rate: 0.9
  • Mutation Rate Step: 0.3
  • Number of Process: 1
  • Number of Experiments: 3
  1. Single Process (with default params):

     python main.py
     

  2. Multiprocessing (with default params):

     python main.py --num_proc n
     

     wtih n number of processes

Timeline

• First Implementation : 2015 ~ 2016 Academic year

• Current Status : March 2017 ~