Epistasis simulator of SNP patterns in Linux
EpistaSim is a Linux 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_Linux” and uncompression through following command:
tar -zxvf EpistaSim_Linux-1.1.0.tar.gz
The summary of arguments are described as follow. If you did not specified the argument value the default or random value will be used.
Where 0 is the ancestor allele and 1 is the derived allele.
|-n||Number of samples in the simulation||30|
|-d||Number of replication of the simulation||1|
|-l||Length of the simulated region (bp)||1000|
|-g||Number of the generation in forward process||200|
|-t||Positions of two selective loci||Random|
|-p||Haplotype frequency with order 00, 01, 10 and 11||Must be specified|
|-R||Recombination rate per generation per bp||3*10(-8)|
|-u||Mutation rate pre generation per bp||3*10(-8)|
|-e||Number of segsites in the simulated region||Random|
|-M||Epistasis model in forward process (M1, M2, M3, M4)||M1|
|-H||Selective Haplotype or allele||11|
|-o||Outputfile of DNA sequence in the simulated region|
|-f||Outputfile of haplotype frequency trajectories|
Simulate the DNA sequences and haplotype frequency through forward process, using fowllowing command:
cd ~/EpistaSim_Linux-1.1.0 python ForWard.py -n 10 -d 5 -l 1000 -g 200 -t 10 100 -p 0.25 0.25 0.25 0.25 -R 0.0000001 -u 0.0000001 -e 10 -M M2 -H 11 -S 0.01 -o forwardsimulation.out -f Hapfre.trac 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. ..........
Simulate the DNA sequences and haplotype frequency through coalescent process, using fowllowing command:
cd ~/EpistaSim_Linux-1.1.0 python BackWard.py -n 10 -d 5 -l 1000 -t 10 100 -p 0.3 0.1 0.1 0.5 -R 0.0000001 -u 0.0000001 -e 10 -H 11 -S 0.01 -o backwardsimulation.out -f Hapfreback.trac 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. ..........
- The arguments except -p can used default value.
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
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