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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/29603?offset=170</link>
	<atom:link href="https://bioinformaticsonline.com/related/29603?offset=170" rel="self" type="application/rss+xml" />
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/24665/national-research-centre-on-plant-biotechnology-for-rajrf-positions</guid>
  <pubDate>Sat, 26 Sep 2015 20:32:49 -0500</pubDate>
  <link></link>
  <title><![CDATA[National Research Centre on Plant Biotechnology for RA/JRF positions]]></title>
  <description><![CDATA[
<p>National Research Centre on Plant Biotechnology - New Delhi, Delhi<br />National Research Centre on Plant Biotechnology recruitments job vacancies for RA/JRF positions</p>

<p>Name of post: Research Associate<br />Salary: Rs.36000/-+ 30% HRA*<br />Educational Qualification: Candidates should have PhD in Biotechnology / Bioinformatics Life Sciences (or) M.Sc Biotechnology / Bioinformatics with three years research experience in relevant field</p>

<p>Name of post: Junior Research Fellow<br />Salary: Rs.25000/-+ 30% HRA*<br />Educational Qualification: Candidates should have M.Sc in Biotechnology /Bioinformatics / Life Sciences with 1st Division or 60% marks or equivalent overall grade point from any recognized professional University</p>

<p>Age Limit: 35 years max. (5 years relaxation for SC/ST/OBC)</p>

<p>How to attend walk in interview?<br />Interested candidates may attend Walk- in-interview on 1st October, 2015 at 10 am at NRCPB, LBS Building, Pusa Campus, and New Delhi-110012 at the above address along with updated Bio-data (CV), ID Proof &amp; attested copies of Certificates and Original to prove qualification &amp; Experience.</p>

<p>Recruitment reference: http://www.nrcpb.org/jobslist</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/24942/bioinformatics-faculty-at-university-of-hyderabad</guid>
  <pubDate>Wed, 14 Oct 2015 22:53:44 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Faculty at UNIVERSITY OF HYDERABAD]]></title>
  <description><![CDATA[
<p>UNIVERSITY OF HYDERABAD</p>

<p>(A Central University established by an Act of Parliament)</p>

<p>Prof. C.R.Rao Road, P.O. Central University Campus, Gachibowli,</p>

<p>Hyderabad - 500 046</p>

<p>Advt.No. UH/HR/Rectt-2015/02 dt. 12.10.2015</p>

<p>The University invites applications from the Indian citizens for the following positions:</p>

<p>Professor / Associate Professor / Assistant Professor :</p>

<p>    Biotechnology &amp; Bioinformatics</p>

<p>Last date : 16th November 2015</p>

<p>More Info : http://www.uohyd.ac.in/images/recruitment/advt-121015.pdf</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25097/teaching-careers-2015-at-uttaranchal-college-of-science-technology</guid>
  <pubDate>Mon, 02 Nov 2015 04:00:26 -0600</pubDate>
  <link></link>
  <title><![CDATA[Teaching Careers 2015 at Uttaranchal College of Science &amp; Technology]]></title>
  <description><![CDATA[
<p>Teaching, Non-teaching Careers 2015<br />Uttaranchal College of Science &amp; Technology - Dehra Dun, Uttarakhand<br />Teaching, Non-teaching Careers 2015 at Uttaranchal College of Science and Technology, Dehradun</p>

<p>Below mentioned teaching and non-teaching job vacancies are to be recruited.</p>

<p>Assistant Professors job vacancies in the disciplines of:<br />Biotechnology<br />Bioinformatics</p>

<p>Eligibility:<br />Masters Degree in the Discipline along with Ph.D</p>

<p>How to apply:<br />Candidates who possess requisite eligibility criteria for all the above mentioned positions required to apply on or before 10 days from the date of vacancy notification.</p>

<p>Candidates required to send copies of all the documents along with application</p>

<p>Contact details:<br />Uttaranchal College of Science &amp; Technology<br />Nagal Hatnala, P.O. Kulhan Sahastradhara Road,<br />Dehradun-248001, Uttarakhand, India</p>

<p>More details can be had at:<br />Dehradun Classifieds e-paper dated 01.11.2015 at page number 40-41</p>

<p>About Employer</p>

<p>Uttaranchal College of Science and Technology, Dehradun, Uttarakhand is affiliated to HNB Garhwal University, Srinagar, Uttarakhand</p>

<p>Employer:	Uttaranchal College of Science &amp; Technology<br />Address:	Uttaranchal College of Science &amp; Technology Nagal Hatnala, P.O. Kulhan Sahastradhara Road, Dehradun-248001, Uttarakhand, India<br />Email:	info@ucstdoon.com<br />URL:	http://www.ucstdoon.com<br />Phone:	0135-2607011, 607413, 3254785, 09719146701</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25150/project-assistant-ii-jobs-opportunity-in-national-chemical-laboratory-ncl-on-temporary-basis</guid>
  <pubDate>Fri, 06 Nov 2015 01:36:16 -0600</pubDate>
  <link></link>
  <title><![CDATA[Project Assistant II Jobs opportunity in National Chemical Laboratory (NCL) on temporary basis]]></title>
  <description><![CDATA[
<p>No. Bio/NCIM/3 </p>

<p>Project Assistant II Jobs opportunity in National Chemical Laboratory (NCL) on temporary basis</p>

<p>Project Code No. : GAP312626</p>

<p>Title of the Project : Microbial ecology and distribution of geochemical cycling genes in an hot spring ecosystem</p>

<p>No. of Post : 01</p>

<p>Qualifications : M.Sc./B.Tech/M.Tech in Computational biology/ Bioinformatics from recognized university with minimum 60 % marks (aggregate) </p>

<p>Desirable : Good knowledge of computational skills, Linux (command line and GUI) and Unix; Perl / Python / R /C-programming. Practical knowledge of analysis of Next generation sequence datasets (amplicon sequencing, whole metagenome, and complete genome sequencing) with reference to microbes. Analysis and statistical validation of NGS data generated from different chemistry platforms. Some wet-lab experience in microbial system would be an added advantage as project involves some travel.</p>

<p>Emoluments : Rs. 16,000/- </p>

<p>Age Limit : 28 years<br />How to apply</p>

<p>The application with the above information duly signed together with photo-copies of relevant certificates/testimonials should be addressed to : The Head, NCIM Resource Centre (Attn Dr. M.S. DHARNE), National Chemical Laboratory, Pune 411 008, so as to reach on or before 16th November 2015.</p>

<p>More at http://www.ncl-india.org/files/JoinUs/JobVacancies/TemporaryJobs.aspx?menuid=ql6&amp;childmenustripid=divSubQL6</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25286/postdoctoral-positions-are-available-at-instem</guid>
  <pubDate>Tue, 24 Nov 2015 23:24:28 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral positions are available at inStem]]></title>
  <description><![CDATA[
<p>A position for a Postdoctoral fellow is available in the area of bioinformatics and genomics. The Institute for Stem Cell Biology and Regenerative Medicine (inStem) is a highly collaborative environment and we are seeking an individual who can interface with both wet and dry lab scientists to use profiling technologies to advance our understanding of tissue regeneration and repair. Consequently, the selected candidate for this position can expect world-class training in integrating the fields of cell biology, molecular biology, animal models, and genomics/proteomics.</p>

<p>We are seeking an individual with expertise in analyzing next generation sequencing data, mutation calling in exome seq data, network inference, data integration, and modeling. Competitive candidates would also have programming experience in scripting languages with perl, C, C++, and R programming. This position requires a PhD in Computational Biology, Bioinformatics, Biostatistics or related fields, and evidence of scientific productivity through publications in international journals. Motivation to gain an in-depth understanding of biological phenomena is required! Applications should include a current CV and names of at least three references. Application packages and inquiries regarding this position can be sent to Dr. Dasaradhi Palakodeti ( dasaradhip@instem.res.in ) or Dr. Colin Jamora ( colinj@instem.res.in). Screening of applications will commence immediately and the position will remain open until filled.</p>

<p>More at https://www.instem.res.in/open-positions</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25309/research-development-informatics-officer</guid>
  <pubDate>Sun, 29 Nov 2015 03:47:34 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research &amp; Development - Informatics Officer]]></title>
  <description><![CDATA[
<p>Research &amp; Development - Informatics Officer<br />Centre for Innovative and Applied Bioprocessing - Mohali, Punjab<br />(Area Coverage: Database and Research Analysis, Documentation, Research Reference, Document &amp; Domain Knowledge Library, Application Programs)<br />Rs. 15600-39100 (PB-3) + Rs. 6600 (Grade Pay)<br />(Higher start within the scale is possible for a deserving case)<br />One Position (Unreserved)<br />Age limit: 45 Years</p>

<p>Essential Qualifications:<br />First class M. Tech or M.E. in computer science or information technology or bioinformatics with 4 years of R&amp;D experience (after Master’s Degree) in an R&amp;D organization with work profile of large data assembly, analysis, and/or customer/user-based software programming and/or, program implementation, database development evidenced by patents and/or publications, credible scale of R&amp;D related data/data sets submission to public database for expanded use etc. Company Info.<br />Centre for Innovative and Applied Bioprocessing</p>

<p>CENTER OF INNOVATIVE AND APPLIED BIOPROCESSING (A National Institute under Dept. of Biotechnology, Ministry of Science &amp; Technology, Govt. of India) 2nd Floor, C-127, Phase VIII, Industrial Area, S.A.S. Nagar, Mohali-160071(Pb). Additional Information States &amp; U.T State &amp; Union Territories Punjab How To Apply Apply Details<br />Apply directly.. Web/Notification URL http://ciab.res.in/vacancies/CIAB-Rollin g%20Advt-2015.pdf</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25409/jrf-bioinformatics-at-cuk</guid>
  <pubDate>Thu, 03 Dec 2015 23:40:38 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF Bioinformatics at CUK]]></title>
  <description><![CDATA[
<p>JRF Bioinformatics</p>

<p>Eligibility : MSc(Bio-Informatics), BE/B.Tech</p>

<p>Location : Kasaragod</p>

<p>Last Date : 20 Dec 2015</p>

<p>Hiring Process : Face to Face Interview<br />Central University of Kerala</p>

<p>JRF job opportunity in Central University of Kerala (CUK) on temporary basis </p>

<p>Project Title : "Targeting TAL effector mediated susceptibility for durable and broad-spectrum resistance to bacterial blight in Rice"</p>

<p>No. of Post : 01</p>

<p>Qualification : MSc in any subject under Life Science or Bioinformatics/ B.Tech in Bioinformatics + 1 yr experience </p>

<p>Stipend : Rs. 14,000/-<br />How to apply</p>

<p>Interested candidates are requested to send their applications explaining their interest in the position with an updated CV to Dr. Ginny Antony, Assistant Professor, Department of Plant Science, School of Biological Sciences, Central University of Kerala, Padannakkad, Kasaragod, Kerala - 671 314 email: ginnycuk2013@gmail.com on or before 20th December, 2015.</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25815/jrf-bioinformatics-job-position-in-university-of-hyderabad</guid>
  <pubDate>Tue, 29 Dec 2015 01:00:18 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF Bioinformatics job position in University of Hyderabad]]></title>
  <description><![CDATA[
<p>JRF Bioinformatics</p>

<p>Eligibility : ME/M.Tech(Bio-Informatics/Bio-Chemistry Engg), MSc(Bio-Informatics)</p>

<p>Location : Hyderabad</p>

<p>Last Date : 30 Dec 2015</p>

<p>Hiring Process : Written-test<br />University of Hyderabad</p>

<p>JRF Bioinformatics job position in University of Hyderabad </p>

<p>Project Entitled : Programming protective humoral responses with novel vaccine formulations against Dengue Virus</p>

<p>Essential Qualifications : M. Sc. in Life Sciences/Bioinformatics/ or M. Tech in Bioinformatics with a minimum of 60% marks and with CSIR-UGC JRF/NET or valid GATE score are preferred. Desirable : Candidates should have six months to one year hands on experience in molecular biology techniques like gene cloning, protein expression and purification, hands on various nano-formulations for drug/vaccine delivery, immunological assays including animal handling, immunizations, T cells and B cell assays or Candidate should have strong background in Bioinformatics and computational Biology, good programming skill particularly proficiency in R/PERL/PYTHON. Candidates interested in above position should send a one page statement clearly explaining how their skills are relevant to the above said position. The candidates should also enclose detailed CV and the name/Email IDs of three references</p>

<p>Fellowship : Rs. 16,000 p.m. + 30% H.R.A. for the first two years (Revised DBT fellowship guidelines maybe applicable)</p>

<p>Duration : The appointment will be on temporary basis for a period of one year. Based on performance, the appointment could be extended till the end of project<br /> <br />How to apply</p>

<p>Submit your application (hardcopy) in a closed envelope to Dr.Nooruddin<br />Khan, Room S-66B,Department of Biotechnology and Bioinfromatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046 or E mail: nklabsls@gmail.com. Last date for receipt of applications is on or before 30.12.2015</p>

<p>More at http://uohyd.ac.in/index.php/component/content/article/87-administration/recruitments/129</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/26432/summer-2016</guid>
  <pubDate>Sun, 21 Feb 2016 06:17:55 -0600</pubDate>
  <link></link>
  <title><![CDATA[Summer 2016]]></title>
  <description><![CDATA[
<p>REU at Fordham University- Summer 2016</p>

<p>An NSF-funded REU to study Y-chromosome diversity and sex-biased dispersal in wild brown rats (Rattus norvegicus) is available in the Munshi-South Lab at Fordham University. Our lab is currently investigating rat evolution at scales ranging from landscape genetics of individual cities to global patterns of diversity. Development of resources for investigating Y-chromosome diversity will support many of these studies. The REU student will work with the lab to bioinformatically identify Y-chromosome SNPs, design SNPtype assays,<br />extract DNA, genotype samples, and analyze data.</p>

<p>We seek applicants interested in bioinformatics, evolutionary biology, and related disciplines.  Applicants must have taken a college-level genetics course.  This REU will require attention to detail, reliability, independence, and critical thinking.</p>

<p>This position is based at Fordham University's field station, the Louis Calder Center, in Armonk, NY. The Calder Center is located approximately 25 miles north of New York City in a protected woodland area. Housing<br />will be provided at the Calder Center for the duration of the REU (May 23 to Aug 12, 2016). Additionally, the student will receive a $6,000 stipend. The selected student will participate in professional development activities through the Calder Centers REU program, including presentation of results at a research colloquium at the end of the summer.</p>

<p>To apply, please send a one page personal statement about your scientific interests and how this REU will support your professional goals, unofficial transcripts including a list of Spring 2016 courses, and names of two professional references (including title, address, phone number, and email address) as a single pdf (with your last name in the file name) to Dr. Jason Munshi-South (jmunshisouth@fordham.edu).</p>

<p>Applications are due March 4th, 2016.</p>

<p>Jason Munshi-South</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/26629/computer-simulation-of-genetic-mechanism</guid>
	<pubDate>Sun, 13 Mar 2016 09:29:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/26629/computer-simulation-of-genetic-mechanism</link>
	<title><![CDATA[Computer simulation of genetic mechanism !!]]></title>
	<description><![CDATA[<p>Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing the execution output. Simulation embodies the principle of ``learning by doing'' --- to learn about the system we must first build a model of some sort and then operate the model. The use of simulation is an activity that is as natural as a child who role plays. Children understand the world around them by simulating (with toys and figurines) most of their interactions with other people, animals and objects. As adults, we lose some of this childlike behavior but recapture it later on through computer simulation. To understand reality and all of its complexity, we must build artificial objects and dynamically act out roles with them. Computer simulation is the electronic equivalent of this type of role playing and it serves to drive synthetic environments and virtual worlds. Within the overall task of simulation, there are three primary sub-fields: model design, model execution and model analysis<br /><br />Simulation models have become important tools in Bioinformatics studies. There are many reasons for this, but we emphasize three of the more important:</p><p>(1) they enable exploration of hypotheses, and as such, have become invaluable means to guide research;</p><p>(2) they are unique approaches to integrate (in the literal term of the word) biological knowledge, in the form of experimental results; and</p><p>(3) they enable connecting biology with other fields of study ranging from physiology to genomics;</p><p>This blog, and this software list, is intended to guide the potential user of simulation models.<br />It is not, in any way, meant to be comprehensive on the very diverse simulation tools that already exist, but focuses on mechanistic, dynamic models. Similarly, it is not meant to provide any coverage of the breadth of applications; however, for interested readers, we provide references to use as a possible starting point.<br /><br />Simulation models are meant to answer questions which scientists have in a dynamic, quantitative, and often, a pictorial way. Much of the bioinformatics research and its applications, in particular, involve a large number of components, actors, and factors. Assembling these in a coherent framework may seem a daunting task, especially for beginners, and can lead to confusion, even for experienced scientists, especially if the objectives of such an exercise are not well defined. Followings are the list of tools bioinformatician may use to analyze and provide answers to complex biological mechanisms and related problems.</p><p style="margin-bottom: 0in;">&nbsp;</p><table width="718" cellspacing="0" cellpadding="2"><colgroup><col width="134"> <col width="501"> </colgroup>
<tbody>
<tr><th style="border: none; padding: 0in;">
<p>Software Resource</p>
</th><th style="border: none; padding: 0in;">
<p>Brief Description and Homepage</p>
</th></tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/aladyn/">Aladyn </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Tools to investigate how demographic parameters, populations genetics and abiotic conditions affect the rate of adaptation <br /><a href="http://www.katja-schiffers.eu/research.html">http://www.katja-schiffers.eu/research.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/alf/">ALF </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A Simulation Framework for Genome Evolution <br /><a href="http://www.cbrg.ethz.ch/alf">http://www.cbrg.ethz.ch/alf</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/art/">ART </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>ART is a set of simulation tools to generate synthetic next-generation sequencing data by mimicking real sequencing process with empirical error models or quality profiles. <br /><a href="http://www.niehs.nih.gov/research/resources/software/biostatistics/art/">http://www.niehs.nih.gov/research/resources/software/biostatistics/art/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/bamsurgeon/">BAMSurgeon </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Methods for realistic simulation of mutations in real data. <br /><a href="https://github.com/adamewing/bamsurgeon">https://github.com/adamewing/bamsurgeon</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/bayesian-serial-simcoal/">Bayesian Serial SimCoal </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. <br /><a href="http://www.stanford.edu/group/hadlylab/ssc/index.html">http://www.stanford.edu/group/hadlylab/ssc/index.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/baysics/">BaySICS </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>An integral platform with a graphical interface for statistical inference based on approximate Bayesian computation. <br /><a href="https://sites.google.com/site/baysicsabc/">https://sites.google.com/site/baysicsabc/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/beers/">BEERS </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data <br /><a href="http://cbil.upenn.edu/BEERS/">http://cbil.upenn.edu/beers/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/bottleneck/">BOTTLENECK </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies <br /><a href="http://www.ensam.inra.fr/URLB/bottleneck/bottleneck.html">http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/bottlesim/">BottleSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>BottleSim is a computer simulation program for simulating the process of population bottlenecks <br /><a href="http://chkuo.name/software/BottleSim.html">http://chkuo.name/software/bottlesim.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/cass/">CASS </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Protein Sequence Simulation <br /><a href="https://liberles.cst.temple.edu/Software/CASS/index.html">https://liberles.cst.temple.edu/software/cass/index.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/cdpop/">CDPOP </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior. <br /><a href="http://cel.dbs.umt.edu/CDPOP">http://cel.dbs.umt.edu/cdpop</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/classical-genetics-simulator/">Classical Genetics Simulator </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Web-based simulation software <br /><a href="http://www.cgslab.com/">http://www.cgslab.com/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/coasim/">CoaSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. <br /><a href="http://users-birc.au.dk/mailund/CoaSim/index.html">http://users-birc.au.dk/mailund/coasim/index.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/cosi/">cosi </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>The cosi package is written in C and is available as a tar file. <br /><a href="http://www.broadinstitute.org/%7Esfs/cosi/">http://www.broadinstitute.org/~sfs/cosi/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/cs-pseq-gen/">CS-PSeq-Gen </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny <br /><a href="http://bioserv.rpbs.univ-paris-diderot.fr/software/CS-PSeq-Gen/">http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/dawg/">DAWG </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>An application designed to simulate the evolution of recombinant DNA sequences in continuous time <br /><a href="http://scit.us/projects/dawg">http://scit.us/projects/dawg</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/easypop/">Easypop </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions <br /><a href="http://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html">http://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/egglib/">EggLib </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>EggLib is a C++/Python library and program package for evolutionary genetics and genomics. <br /><a href="http://egglib.sourceforge.net/">http://egglib.sourceforge.net/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/episim/">EpiSIM </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis <br /><a href="https://sourceforge.net/projects/episimsimulator/files/">https://sourceforge.net/projects/episimsimulator/files/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/evolsimulator/">EvolSimulator </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A simulation test bed for hypotheses of genome evolution <br /><a href="http://acb.qfab.org/acb/evolsim/">http://acb.qfab.org/acb/evolsim/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/evolveagene/">EvolveAGene </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions <br /><a href="http://bellinghamresearchinstitute.com/software/index.html">http://bellinghamresearchinstitute.com/software/index.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/fastsimcoal/">fastsimcoal </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A continuous-&shy;‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios <br /><a href="http://cmpg.unibe.ch/software/fastsimcoal/">http://cmpg.unibe.ch/software/fastsimcoal/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/fastslink/">FastSLINK </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Simulation of Marker and Phenotype Data in Pedigrees <br /><a href="https://watson.hgen.pitt.edu/">https://watson.hgen.pitt.edu/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/ffpopsim/">FFPopSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>C++/Python library for population genetics. <br /><a href="http://webdav.tuebingen.mpg.de/ffpopsim/">http://webdav.tuebingen.mpg.de/ffpopsim/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/flux-simulator/">FLUX SIMULATOR </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. <br /><a href="http://sammeth.net/confluence/display/SIM/Home">http://sammeth.net/confluence/display/sim/home</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/forqs/">forqs </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Forward-in-time simulation of Recombination, Quantitative Traits, and Selection <br /><a href="https://bitbucket.org/dkessner/forqs">https://bitbucket.org/dkessner/forqs</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/forsim/">ForSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>ForSim: A Forward Evolutionary Computer Simulation <br /><a href="http://anth.la.psu.edu/research/weiss-lab/research/research">http://anth.la.psu.edu/research/weiss-lab/research/research</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/forwsim/">ForwSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process. <br /><a href="http://badri-populationgeneticsimulators.blogspot.com/">http://badri-populationgeneticsimulators.blogspot.com/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/fpg/">FPG </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Forward Population Genetic simulation <br /><a href="https://bio.cst.temple.edu/%7Ehey/software/software.htm#FPG">https://bio.cst.temple.edu/~hey/software/software.htm#fpg</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/fregene/">FREGENE </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. <br /><a href="http://www.ebi.ac.uk/projects/BARGEN">http://www.ebi.ac.uk/projects/bargen</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/frequency-based-insilico-genome-generator-figg/">FIGG </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>FIGG is a genome simulation tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC content across a genome to model new genomes in FASTA format while tracking applied mutations for use in analysis <br /><a href="http://insilicogenome.sourceforge.net/">http://insilicogenome.sourceforge.net/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/fwdpp/">fwdpp </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A C++ template library for implementing efficient forward simulations. <br /><a href="http://molpopgen.github.io/fwdpp/">http://molpopgen.github.io/fwdpp/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/gametes/">GAMETES </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. <br /><a href="http://sourceforge.net/projects/gametes/?source=navbar">http://sourceforge.net/projects/gametes/?source=navbar</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/gasp/">GASP </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. <br /><a href="http://research.nhgri.nih.gov/gasp/">http://research.nhgri.nih.gov/gasp/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/gcta/">GCTA </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Genome-wide Complex Trait Analysis <br /><a href="http://www.complextraitgenomics.com/software/gcta/download.html">http://www.complextraitgenomics.com/software/gcta/download.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/gemsim/">GemSIM </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Next generation sequencing read simulator <br /><a href="http://sourceforge.net/projects/gemsim/">http://sourceforge.net/projects/gemsim/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/geneartisan/">GeneArtisan </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Simulation of Markers in Case-Control Study Designs <br /><a href="http://www.rannala.org/?page_id=241">http://www.rannala.org/?page_id=241</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/genome/">GENOME </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A rapid coalescent-based whole genome simulator <br /><a href="http://www.sph.umich.edu/csg/liang/genome/">http://www.sph.umich.edu/csg/liang/genome/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/genomepop2/">GenomePop2 </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version. <br /><a href="https://ritchielab.psu.edu/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla">https://ritchielab.psu.edu/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/genomesimla/">GenomeSimla </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested <br /><a href="http://chgr.mc.vanderbilt.edu/genomeSIMLA/">http://chgr.mc.vanderbilt.edu/genomesimla/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/gens2/">GENS2 </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. <br /><a href="https://sourceforge.net/projects/gensim/">https://sourceforge.net/projects/gensim/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/gwasimulator/">GWAsimulator </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A rapid whole genome simulation program <br /><a href="http://biostat.mc.vanderbilt.edu/wiki/Main/GWAsimulator">http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/hap-sample/">HAP-SAMPLE </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>An association simulator for candidate regions or genome scans <br /><a href="http://www.hapsample.org/">http://www.hapsample.org/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/hapgen/">HAPGEN </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A simulator for the simulation of case control datasets at SNP markers <br /><a href="https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html">https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/hapsim/">HapSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients <br /><a href="http://cran.r-project.org/web/packages/hapsim/index.html">http://cran.r-project.org/web/packages/hapsim/index.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/hapsimu/">HAPSIMU </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model <br /><a href="http://l.web.umkc.edu/liujian/">http://l.web.umkc.edu/liujian/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/ibdsim/">IBDsim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models. <br /><a href="http://raphael.leblois.free.fr/">http://raphael.leblois.free.fr/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/indel-seq-gen/">indel-Seq-Gen </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies <br /><a href="http://bioinfolab.unl.edu/%7Ecstrope/iSG/">http://bioinfolab.unl.edu/~cstrope/isg/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/indelible/">Indelible </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A powerful and flexible simulator of biological evolution <br /><a href="http://abacus.gene.ucl.ac.uk/software/indelible/">http://abacus.gene.ucl.ac.uk/software/indelible/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/invertfregene/">invertFREGENE </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>InvertFREGENE is a forward-in-time simulator of inversions in population genetic data <br /><a href="http://www.ebi.ac.uk/projects/BARGEN/">http://www.ebi.ac.uk/projects/bargen/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/kernalpop/">kernalPop </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A spatially explicit population genetic simulation engine <br /><a href="http://cran.r-project.org/src/contrib/Archive/kernelPop/">http://cran.r-project.org/src/contrib/archive/kernelpop/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/macs/">MaCS </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Markovian Coalescent Simulator <br /><a href="http://www-hsc.usc.edu/%7Egarykche/">http://www-hsc.usc.edu/~garykche/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/marlin/">Marlin </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Marlin provides a user-friendly interface for performing forward-in-time population genetic simulations. <br /><a href="http://www.patrickmeirmans.com/software/Marlin.html">http://www.patrickmeirmans.com/software/marlin.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/mason/">Mason </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A package for the simulation of nucleotide data. <br /><a href="http://www.seqan.de/projects/mason/">http://www.seqan.de/projects/mason/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/mbs/">mbs </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection <br /><a href="http://www.sendou.soken.ac.jp/esb/innan/InnanLab/software.html">http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/mendels-accountant/">Mendel's Accountant </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine <br /><a href="http://mendelsaccount.sourceforge.net/">http://mendelsaccount.sourceforge.net/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/metapopgen/">MetaPopGen </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Simulates genetics in large size metapopulations <br /><a href="https://sites.google.com/site/marcoandrello/metapopgen">https://sites.google.com/site/marcoandrello/metapopgen</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/metasim/">MetaSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets <br /><a href="http://ab.inf.uni-tuebingen.de/software/metasim/">http://ab.inf.uni-tuebingen.de/software/metasim/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/mlcoalsim/">mlcoalsim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Multilocus Coalescent Simulations <br /><a href="http://code.google.com/p/mlcoalsim-v1/">http://code.google.com/p/mlcoalsim-v1/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/ms/">ms </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. <br /><a href="http://home.uchicago.edu/%7Erhudson1/source/mksamples.html">http://home.uchicago.edu/~rhudson1/source/mksamples.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/mshot/">msHOT </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. <br /><a href="http://home.uchicago.edu/%7Erhudson1/">http://home.uchicago.edu/~rhudson1/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/msms/">msms </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A coalescent Simlation tool with selection. <br /><a href="http://www.mabs.at/ewing/msms/index.shtml">http://www.mabs.at/ewing/msms/index.shtml</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/myssp/">MySSP </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A program for the simulation of DNA sequence evolution across a phylogenetic tree <br /><a href="http://www.rosenberglab.net/software.html">http://www.rosenberglab.net/software.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/nemo/">Nemo </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework. <br /><a href="http://nemo2.sourceforge.net/">http://nemo2.sourceforge.net/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/netrecodon/">NetRecodon </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography <br /><a href="http://code.google.com/p/netrecodon/">http://code.google.com/p/netrecodon/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/">OncoSimulR </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>BioConductor package for Forward Genetic Simulation of Cancer Progresion with Epistasis <br /><a href="https://github.com/rdiaz02/OncoSimul">https://github.com/rdiaz02/oncosimul</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/pedagog/">PEDAGOG </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Software for simulating eco-evolutionary population dynamics <br /><a href="https://bcrc.bio.umass.edu/pedigreesoftware/node/5">https://bcrc.bio.umass.edu/pedigreesoftware/node/5</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/phenosim/">phenosim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A tool to add phenotypes to simulated genotypes <br /><a href="http://evoplant.uni-hohenheim.de/doku.php?id=software:software">http://evoplant.uni-hohenheim.de/doku.php?id=software:software</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/phylosim/">PhyloSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>An R package for the Monte Carlo simulation of sequence evolution <br /><a href="http://www.ebi.ac.uk/goldman-srv/phylosim/">http://www.ebi.ac.uk/goldman-srv/phylosim/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/pirs/">pIRS </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Profile-based Illumina pair-end reads simulator <br /><a href="https://code.google.com/p/pirs/">https://code.google.com/p/pirs/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/proteinevolver/">ProteinEvolver </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Simulation of protein evolution along phylogenies under structure-based substitution models <br /><a href="http://code.google.com/p/proteinevolver/">http://code.google.com/p/proteinevolver/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/qmsim/">QMSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>QTL and Marker Simulator <br /><a href="http://www.aps.uoguelph.ca/%7Emsargol/qmsim/">http://www.aps.uoguelph.ca/~msargol/qmsim/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/quantinemo/">quantiNEMO </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population <br /><a href="http://www2.unil.ch/popgen/softwares/quantinemo/">http://www2.unil.ch/popgen/softwares/quantinemo/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/recoal/">RECOAL </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Simulates new haplotype data from a reference population of haplotypes. <br /><a href="ftp://popgen.usc.edu/">ftp://popgen.usc.edu/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/recodon/">Recodon </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Coalescent simulation of coding DNA sequences with recombination, migration and demography <br /><a href="http://code.google.com/p/recodon/">http://code.google.com/p/recodon/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/rlsim/">rlsim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A package for simulating RNA-seq library preparation with parameter estimation <br /><a href="http://bit.ly/rlsim-git">http://bit.ly/rlsim-git</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/rmetasim/">Rmetasim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R <br /><a href="http://cran.r-project.org/web/packages/rmetasim/index.html">http://cran.r-project.org/web/packages/rmetasim/index.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/rna-seq-simulator/">RNA Seq Simulator </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. <br /><a href="http://useq.sourceforge.net/cmdLnMenus.html#RNASeqSimulator">http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/rose/">Rose </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Random model of sequence evolution <br /><a href="http://bibiserv.techfak.uni-bielefeld.de/rose/">http://bibiserv.techfak.uni-bielefeld.de/rose/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/scrm/">scrm </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A coalescent simulator optimized for long sequences and large samples. <br /><a href="https://scrm.github.io/">https://scrm.github.io/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/selsim/">SelSim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection <br /><a href="http://www.well.ox.ac.uk/%7Espencer/SelSim/">http://www.well.ox.ac.uk/~spencer/selsim/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/seq-gen/">Seq-Gen </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. <br /><a href="http://tree.bio.ed.ac.uk/software/seqgen/">http://tree.bio.ed.ac.uk/software/seqgen/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/seqpower/">SEQPower </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Statistical power analysis for sequence-based association studies <br /><a href="http://bioinformatics.org/spower/">http://bioinformatics.org/spower/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/seqsimla/">SeqSIMLA </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. <br /><a href="http://seqsimla.sourceforge.net/">http://seqsimla.sourceforge.net/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/serial-netevolve/">Serial NetEvolve </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A flexible utility for generating serially-sampled sequences along a tree or recombinant network <br /><a href="http://biorg.cis.fiu.edu/SNE/">http://biorg.cis.fiu.edu/sne/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/sfs_code/">SFS_CODE </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects. <br /><a href="http://sfscode.sourceforge.net/SFS_CODE/index/index.html">http://sfscode.sourceforge.net/sfs_code/index/index.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/sibsim/">SIBSIM </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Quantitative phenotype simulation in extended pedigrees <br /><a href="http://sourceforge.net/projects/sibsim/">http://sourceforge.net/projects/sibsim/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/simadapt/">SimAdapt </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A spatially explicit, individual-based, forward-time, landscape-genetic simulation model combined with a landscape cellular automaton. <br /><a href="https://www.openabm.org/model/3137">https://www.openabm.org/model/3137</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/simcoal2/">SIMCOAL2 </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models <br /><a href="http://cmpg.unibe.ch/software/simcoal2/">http://cmpg.unibe.ch/software/simcoal2/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/simcopy/">SimCopy </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>An R package simulating the evolution of copy number profiles along a tree. <br /><a href="http://bit.ly/simcopy">http://bit.ly/simcopy</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/simla/">SIMLA </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies. <br /><a href="http://dmpi.duke.edu/simla-simulation-software-version-32">http://dmpi.duke.edu/simla-simulation-software-version-32</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/simped/">SimPed </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures <br /><a href="http://bioinformatics.org/simped/">http://bioinformatics.org/simped/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/simprot/">Simprot </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A program to simulate protein evolution by substitution, insertion and deletion <br /><a href="http://www.uhnresearch.ca/labs/tillier/software.htm#3">http://www.uhnresearch.ca/labs/tillier/software.htm#3</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/simrare/">SimRare </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Rare variant simulation and analysis tool <br /><a href="http://code.google.com/p/simrare/">http://code.google.com/p/simrare/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/simugwas/">simuGWAS </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A forward-time simulator that simulates realistic samples for genome-wide association studies. <br /><a href="http://simupop.sourceforge.net/Cookbook/SimuGWAS">http://simupop.sourceforge.net/cookbook/simugwas</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/simupop/">simuPOP </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. <br /><a href="http://simupop.sourceforge.net/">http://simupop.sourceforge.net/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/sissi/">SISSI </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices. <br /><a href="http://www.cibiv.at/software/sissi/">http://www.cibiv.at/software/sissi/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/smartpop/">SMARTPOP </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Simulating Mating Alliance as a Reproductive Tactic for Populations <br /><a href="http://smartpop.sourceforge.net/">http://smartpop.sourceforge.net/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/snpsim/">SNPsim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Coalescent simulation of hotspot recombination <br /><a href="http://code.google.com/p/phylosoftware/">http://code.google.com/p/phylosoftware/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/spip/">SPIP </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user <br /><a href="http://swfsc.noaa.gov/textblock.aspx?Division=FED&amp;id=3434">http://swfsc.noaa.gov/textblock.aspx?division=fed&amp;id=3434</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/splatche/">Splatche </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Spatial and Temporal Coalescences in Heterogeneous Environment <br /><a href="http://www.splatche.com/">http://www.splatche.com/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/srv/">srv </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. <br /><a href="http://simupop.sourceforge.net/Cookbook/SimuRareVariants">http://simupop.sourceforge.net/cookbook/simurarevariants</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/sup/">SUP </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>SLINK/FastSLINK utility program <br /><a href="http://mlemire.freeshell.org/software.html">http://mlemire.freeshell.org/software.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/treesimj/">TreesimJ </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A flexible, forward-time population genetic simulator <br /><a href="http://code.google.com/p/treesimj/">http://code.google.com/p/treesimj/</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/variant-simulation-tools/">Variant Simulation Tools </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>A simulation tool for post-GWAS genetic epidemiological studies using whole-genome or whole-exome next-gen sequencing data, with an emphasis on user-friendliness and reproducibility. <br /><a href="http://varianttools.sourceforge.net/Simulation/HomePage">http://varianttools.sourceforge.net/simulation/homepage</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/vortex/">Vortex </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>VORTEX is an individual-based simulation model for population viability analysis (PVA). <br /><a href="http://www.vortex9.org/vortex.html">http://www.vortex9.org/vortex.html</a></p>
</td>
</tr>
<tr><th style="border: none; padding: 0in;">
<p><a href="https://popmodels.cancercontrol.cancer.gov/gsr/packages/wessim/">Wessim </a></p>
</th>
<td style="border: none; padding: 0in;">
<p>Whole Exome Sequencing SIMulator <br /><a href="http://sak042.github.io/Wessim/">http://sak042.github.io/wessim/</a></p>
</td>
</tr>
</tbody>
</table><p style="margin-bottom: 0in;">&nbsp;</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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