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Project Description

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

Run EpistaSim

Options:

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.

Switch Argument Comments(Default)
-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
-S Slective Coefficient  
-o Outputfile of DNA sequence in the simulated region  
-f Outputfile of haplotype frequency trajectories  

Forward Example:

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.

..........

Backward:

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.

..........
Note
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
Release History

Release History

1.1.0

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
EpistaSim_Linux-1.1.0.tar.gz (19.3 kB) Copy SHA256 Checksum SHA256 Source Jul 22, 2015

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