{ "info": { "author": "Shaojun Zhang", "author_email": "zhangshaojun@ems.hrbmu.edu.cn", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Win32 (MS Windows)", "Intended Audience :: Science/Research", "License :: OSI Approved :: Python Software Foundation License", "Natural Language :: English", "Operating System :: Microsoft :: Windows", "Operating System :: Microsoft :: Windows :: Windows 7", "Operating System :: Microsoft :: Windows :: Windows NT/2000", "Operating System :: Microsoft :: Windows :: Windows XP", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7", "Topic :: Software Development :: Build Tools" ], "description": "===============\r\nEpistaSim_wins\r\n===============\r\n\r\nEpistaSim 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. \r\nThe 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 \r\n(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. \r\n\r\n\r\n-------------------------\r\n**Download and Install**\r\n-------------------------\r\n\r\nDownload package \"EpistaSim\" and unzip\r\n\r\nRun cmd and enter the directory of EpistaSim\r\n\r\nLoading EpistaSim package, use following command:\r\n \r\n ::\r\n \r\n python setup.py install\r\n\r\n\r\n------------------\r\n**Run EpistaSim**\r\n------------------\r\n\r\nOpen the window of python (Commond line) or Python Shell\r\n\r\n\r\n*Forward:*\r\n^^^^^^^^^^^^^^^^^^^^^\r\n\r\n\r\nSimulate the DNA sequences and haplotype frequency through forward process, using fowllowing command:\r\n \r\n ::\r\n \r\n import Forward\r\n Forward.main()\r\n \r\n \r\n*Examples:* \r\n ::\r\n \r\n import Forward\r\n Forward.main()\r\n\r\n A prompt of input arguments as follow:\r\n Enter haplotype frequency split by space: 0.25 0.25 0.25 0.25\r\n \r\n Enter Epistasis selective model (If you want to use default value press space key): M1\r\n \r\n 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\r\n \r\n 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\r\n \r\n Enter the number of simulated samples ( If you want to use default value press space key): 10\r\n \r\n Enter the number of replication ( If you want to use default value press space key): 5\r\n \r\n Enter the length of simulated region ( If you want to use default value press space key): 1000\r\n \r\n Enter the number of generation ( If you want to use default value press space key): 200\r\n \r\n Enter position of two selective loci split by space ( If you want to use random position press space key): 10 100\r\n \r\n Enter recombination rate per generation per bp ( If you want to use default value press space key): \r\n \r\n Enter mutation rate per generation per bp ( If you want to use default value press space key): 0.0000001\r\n \r\n Enter the number of segsites in the region ( If you want to use random value press space key): \r\n \r\n Enter the outputfile name of simulated sequence: forward.out\r\n \r\n Enter the outputfile name of haplotype frequency trajectories: hapfre.out\r\n \r\n The running information of Forward was illustrated as follow:\r\n \r\n Generate the initial population\r\n \r\n Print the track file of haplotype frequency\r\n \r\n Simulation the offspring\r\n \r\n simulation the 0th replication\r\n \r\n A region of 1000bp include 12 segsites were simulated for 200 generations with sample size 10 for 1 replication.\r\n \r\n ..........\r\n \r\n\r\n*Backward:*\r\n^^^^^^^^^^^^^^^^^^^^^\r\n\r\nSimulate the DNA sequences and haplotype frequency through coalescent process, using fowllowing command:\r\n \r\n ::\r\n \r\n import Backward\r\n Backward.main()\r\n \r\n \r\n*Examples*\r\n \r\n ::\r\n \r\n import Backward\r\n Backward.main()\r\n\r\n A prompt of input arguments as follow:\r\n Enter haplotype frequency split by space: 0.3 0.1 0.1 0.5\r\n \r\n Enter selective haplotype from two-locus(If you want to use default value press space key): 11\r\n \r\n Enter selective coefficient ( If you want to use default value press space key): 0.01\r\n \r\n Enter the number of simulated samples ( If you want to use default value press space key): 10\r\n \r\n Enter the number of replication ( If you want to use default value press space key): 5\r\n \r\n Enter the length of simulated region ( If you want to use default value press space key): 1000\r\n \r\n Enter position of two selective loci split by space ( If you want to use random position press space key): 10 100\r\n \r\n Enter recombination rate per generation per bp ( If you want to use default value press space key): 0.0000001\r\n \r\n Enter mutation rate per generation per bp ( If you want to use default value press space key): 0.0000001\r\n \r\n Enter the number of segsites in the region ( If you want to use random value press space key): \r\n \r\n Enter the outputfile name of simulated sequence: backward.out\r\n \r\n Enter the outputfile name of haplotype frequency trajectories: hapfre.out\r\n \r\n The running information of Forward was illustrated as follow:\r\n \r\n \r\n Print the track file of haplotype frequency\r\n \r\n Simulation the offspring\r\n \r\n simulation the 0th replication\r\n \r\n A region of 1000bp include 9 segsites were simulated with sample size 10 for 1 replication.\r\n \r\n ..........\r\n \r\n------------------------\r\n**Output of EpistaSim**\r\n------------------------\r\nThe outputs of Forward and Backward are the sames and similar with Hudson's ms software (Hudson, 1990).\r\n\r\nAccording to the up arguments, the results as fowllow:\r\n\r\n \r\n*Output of DNA sequence*\r\n^^^^^^^^^^^^^^^^^^^^^^^^^\r\n \r\n ::\r\n \r\n //\r\n Segsites: 12\r\n Selected two_locus: 10 100 \r\n Positions: 10 100 125 158 258 309 472 631 756 818 858 886 \r\n 111011011111\r\n 111011011110\r\n 111010010110\r\n 111111000111\r\n 111001011011\r\n 101100011111\r\n 001110011111\r\n 001000011111\r\n 001011011111\r\n 011100000001\r\n //\r\n ........\r\n \r\n*Output of haplotype frequency*\r\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n \r\n ::\r\n \r\n //\r\n T\t00\t01\t10\t11\r\n 0\t0.25\t0.25\t0.25\t0.25\t\r\n 1\t0.248079102592\t0.253290720757\t0.254300434135\t0.244329742516\t\r\n 2\t0.250079789017\t0.260533576401\t0.254926425626\t0.234460208956\t\r\n 3\t0.247683161282\t0.257852724706\t0.259331708331\t0.235132405681\t\r\n ......\r\n 199\t0.174483716477\t0.147128461696\t0.166087155013\t0.512300666814\t\r\n 200\t0.175953877557\t0.145569161198\t0.163958437969\t0.514518523277", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://blog.useasp.net/", 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