https://github.com/thibaultlatrille/redqueen

The Red-Queen model of recombination hot-spot evolution: a theoretical investigation.
https://github.com/thibaultlatrille/redqueen

mathematical-modelling scientific-publications simulation

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The Red-Queen model of recombination hot-spot evolution: a theoretical investigation.

• Host: GitHub
• URL: https://github.com/thibaultlatrille/redqueen
• Owner: ThibaultLatrille
• Created: 2016-01-25T07:57:47.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2022-03-22T13:42:17.000Z (over 3 years ago)
• Last Synced: 2025-01-22T17:39:47.719Z (10 months ago)
• Topics: mathematical-modelling, scientific-publications, simulation
• Language: TeX
• Homepage: https://doi.org/10.1098/rstb.2016.0463
• Size: 105 MB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
**The Red-Queen model of recombination hot-spot evolution: a theoretical investigation,**\

_Thibault Latrille, Laurent Duret, Nicolas Lartillot_,\

Phil. Trans. R. Soc. B,\

http://doi.org/10.1098/rstb.2016.0463

#### Code to reproduce the figures showed in the manuscript

Requirements:

 - Python 3.5

 - numpy

 - scipy

 - matplotlib

```

$ python3 redQueen.py -n 100000

```

optional arguments:

  - -c , --cpu 

  

                        Number of CPU available for parallel computing

                        (default: 4)

  - -t , --time 

  

                        The number of steps of simulations (proportional to

                        time) (default: 50)

  - -w , --wall_time 

  

                        The wall time (in seconds) of the whole computation

                        (default: inf)

  - -r , --range 

  

                        The order of magnitude to span around the focal

                        parameters (default: 2)

  - -s , --simulations 

  

                        number of independent simulations to span (default:

                        32)

  - -n , --population_size 

  

                        Effective population size (default: 100000)

  - -u , --mutation_rate_prdm9 

  

                        The mutation rate of Prdm9 (multiplied by 10e-6)

                        (default: 1.0)

  - -v , --mutation_rate_hotspot 

  

                        The mutation rate of hotspots (multiplied by 10e-7)

                        (default: 10.0)

  - -f , --fitness 

  

                        The fitness either 'linear', 'sigmoid', 'power' or

                        'poisson' (default: power)

  - -a , --alpha 

  

                        The parameter alpha of the fitness (default: 0.1)

                        

                        - is not used if the fitness is 'linear'.

                        - is the power exponent if the fitness is 'power'.

                        - is the exponential parameter if the fitness is 'poisson'.

                        - is the inflexion point if the fitness is 'sigmoid'. 

  - -d , --redraw 

  

                        Draw the figures using the file 'Batch.p' (default:

                        False)