Forward:

Simulate the DNA sequences and haplotype frequency through forward process, using fowllowing command:

import Forward
Forward.main()

Examples:

import Forward
Forward.main()

A prompt of input arguments as follow:
          Enter haplotype frequency split by space: 0.25 0.25 0.25 0.25

          Enter Epistasis selective model (If you want to use default value press space key): M1

          Enter selective haplotype or allele from two-locus(You must seperate by comma between alleles from two-locus corresponding to M3 or M4; If you want to use default value press space key): 11

          Enter selective coefficient (If you specified M3 or M4, input two selective coefficients from two locus seperated by comma; If you want to use default value press space key): 0.01

          Enter the number of simulated samples ( If you want to use default value press space key): 10

          Enter the number of replication ( If you want to use default value press space key): 5

          Enter the length of simulated region ( If you want to use default value press space key): 1000

          Enter the number of generation ( If you want to use default value press space key): 200

          Enter position of two selective loci  split by space ( If you want to use random position press space key): 10 100

          Enter recombination rate per generation per bp ( If you want to use default value press space key):

          Enter mutation rate per generation per bp ( If you want to use default value press space key): 0.0000001

          Enter the number of segsites in the region ( If you want to use random value press space key):

          Enter the outputfile name of simulated sequence: forward.out

          Enter the outputfile name of haplotype frequency trajectories: hapfre.out

The running information of Forward was illustrated as follow:

Generate the initial population

Print the track file of haplotype frequency

Simulation the offspring

simulation the 0th replication

A region of 1000bp include 12 segsites were simulated for 200 generations with sample size 10 for 1 replication.

..........

Backward:

Simulate the DNA sequences and haplotype frequency through coalescent process, using fowllowing command:

import Backward
Backward.main()

Examples

import Backward
Backward.main()

A prompt of input arguments as follow:
          Enter haplotype frequency split by space: 0.3 0.1 0.1 0.5

          Enter selective haplotype from two-locus(If you want to use default value press space key): 11

          Enter selective coefficient ( If you want to use default value press space key): 0.01

          Enter the number of simulated samples ( If you want to use default value press space key): 10

          Enter the number of replication ( If you want to use default value press space key): 5

          Enter the length of simulated region ( If you want to use default value press space key): 1000

          Enter position of two selective loci  split by space ( If you want to use random position press space key): 10 100

          Enter recombination rate per generation per bp ( If you want to use default value press space key): 0.0000001

          Enter mutation rate per generation per bp ( If you want to use default value press space key): 0.0000001

          Enter the number of segsites in the region ( If you want to use random value press space key):

          Enter the outputfile name of simulated sequence: backward.out

          Enter the outputfile name of haplotype frequency trajectories: hapfre.out

The running information of Forward was illustrated as follow:


Print the track file of haplotype frequency

Simulation the offspring

simulation the 0th replication

A region of 1000bp include 9 segsites were simulated  with sample size 10 for 1 replication.

..........

Output of DNA sequence

//
Segsites: 12
Selected two_locus: 10 100
Positions: 10 100 125 158 258 309 472 631 756 818 858 886
111011011111
111011011110
111010010110
111111000111
111001011011
101100011111
001110011111
001000011111
001011011111
011100000001
//
........

Output of haplotype frequency

//
T  00      01      10      11
0  0.25    0.25    0.25    0.25
1  0.248079102592  0.253290720757  0.254300434135  0.244329742516
2  0.250079789017  0.260533576401  0.254926425626  0.234460208956
3  0.247683161282  0.257852724706  0.259331708331  0.235132405681
......
199        0.174483716477  0.147128461696  0.166087155013  0.512300666814
200        0.175953877557  0.145569161198  0.163958437969  0.514518523277