EpistaSim_Linux 1.1.0
Epistasis simulator of SNP patterns in Linux
License: MIT
Keywords: Epistasis simulation

=================
EpistaSim_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


------------------
**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