EpistaSim_Windows 1.1.0

Epistasis simulator of SNP pattern in Windows

EpistaSim is a simulator that can estimate haplotype frequency and simulate DNA sequences in a region linking with target two loci under haplotype selective model through forward and backward process integrating with mutation and recombination. The output of software was similar with Hudson’s ms software (Hudson, 1990). EpistaSim is a flexible simulator so that it can incorporate different epistasis model. The software runs forward and coalescent simulations depending on the histories (trajectories) of haplotype frequency which was output accompany with DNA sequences of the region in text files. EpistaSim included two parts forward and backward simulation.

Download and Install

Download package “EpistaSim” and unzip

Run cmd and enter the directory of EpistaSim

Loading EpistaSim package, use following command:

python setup.py install

Run EpistaSim

Open the window of python (Commond line) or Python Shell

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 EpistaSim

The outputs of Forward and Backward are the sames and similar with Hudson’s ms software (Hudson, 1990).

According to the up arguments, the results as fowllow:

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