gerstung-lab / clonex

Efficient Wright-Fisher simulations for intra-tumour population genetics

clonex

This archive contains a C programme to calculate a Wright-Fisher model of cancer development.

Background

This tools models a population growing exponentially from size n to N in g generations. It allows to specify d driver sites with selective advantage s; p passenger sites, which are neutral and o other sites with selective advantage t. Sites mutate at rates u (drivers, other sites) and v, respectively.

Installation

As easy as

$ make

Running

As easy as

$ ./clonex -h
usage: clonex [-N:n:u:v:s:t:g:R:f:r:p:d:o:wh]
  N - Final population size (default = 1000000000)
  n - Initial population size (default = 1)
  u - Mutation rate (default = 1e-07)
  v - Mutation rate passengers (default = u)
  s - Selective advantage (default = 0.01)
  t - Selective advantage of other drivers (default = 0.015)
  g - Number of generations (default = 1800)
  d - Number of drivers (default = 1000)
  p - Number of passengers (default = 0)
  o - Number of other drivers (default = 0)
  R - Replicates (default = 1)
  r - Random seed (default = time)
  f - File directory (Required! Make sure that the directory exists!)
  G - Output every G generations (default = g)
  h - This help
  
$ ./clonex -N 1000000 -n 1000000 -s 0.01 -d 1000 -u 1e-9 -f foo -p 1000000 -v 1e-8 -g 2000