BOL: Related items

The Rogers Lab

Mon, 15 Jul 2019 08:07:44 -0500

The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.

More at http://evolscientist.com/

What is the hologenome concept of evolution?

Jit — Wed, 03 Feb 2021 12:23:54 -0600

All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host–microbiome ecosystem as a “holobiont”.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198262/

Useful link to teach evolution !

Abhi — Wed, 05 Oct 2022 18:29:30 -0500

Mimicry and other resources
Mimicry games:
Great Heliconius game:
http://heliconius.org/evolving_butterflies/
(See also 
https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0014)
Other one, a bit less friendly:
https://ccl.northwestern.edu/netlogo/models/Mimicry
Camouflage practical
https://alexis-catherine.github.io/publication/natural-selection-and-camouflage/
(NetLogo also has one: 
https://ccl.northwestern.edu/netlogo/models/BugHuntCamouflage)
Peppered moth game:
https://askabiologist.asu.edu/peppered-moths-game/play.html

General resources
The always popular Populus:
https://cbs.umn.edu/populus/overview
Drift & Gene Flow 
https://cartwrig.ht/apps/genie/
(Cock van Oosterhout has a great ppt to lead students through this)
See also https://cartwrig.ht/apps/redlynx/
https://demonstrations.wolfram.com/ReplicatorMutatorDynamicsWithThreeStrategies/
NetLogo:
http://ccl.northwestern.edu/netlogo/models/index.cgi
Population Genetics:
https://www.radford.edu/~rsheehy/Gen_flash/popgen/
Evolution in general
https://evolution.berkeley.edu/evolibrary/home.php
Mitochondrial Eve:
https://projects.ncsu.edu/cals/gn/ex/mit-eve.html
Y chromosomes:
https://projects.ncsu.edu/cals/gn/ex/y-chrom.html
A professional online package from Michael Kasumovic:
https://arludo.com/
a compilation of resources:
https://planted.botany.org/index.php?P=Home
Finally, Donald Forsdyke has some great on-line videos explaining
evolutionary principles (occasionally in a fake Scottish accent):
http://post.queensu.ca/~forsdyke/videolectures.htm

When Chromosomes Shift: Understanding Chromosome Rearrangement and Human Disease

BioStar — Fri, 11 Apr 2025 01:07:17 -0500

In the vast and complex world of genetics, our chromosomes are like carefully arranged bookshelves — each holding critical information that defines who we are. But what happens when those books are shuffled, inverted, or swapped? The answer lies in a phenomenon known as chromosome rearrangement, a powerful force behind many human diseases, from developmental disorders to cancer.

What Are Chromosome Rearrangements?

Chromosome rearrangements are structural changes that alter the normal configuration of chromosomes. These changes can involve large segments of DNA — from thousands to millions of base pairs — and can occur spontaneously, be inherited, or result from exposure to mutagens (like radiation or chemicals).

Common Types of Rearrangements:

Deletions – Loss of a chromosome segment
Duplications – Repetition of a segment
Inversions – A segment breaks off, flips, and reattaches
Translocations – Segments exchange places between non-homologous chromosomes
Insertions – A segment is inserted into another part of the genome

These changes can disrupt genes directly or affect gene regulation, leading to disease.

How Do Chromosome Rearrangements Cause Disease?

The impact of a rearrangement depends on which genes are involved, how much DNA is affected, and when the rearrangement occurs (in development vs. adulthood). Here are some key mechanisms:

Gene disruption: Breaking a gene can lead to loss of function or the creation of a non-functional protein.
Gene fusion: Joining parts of two genes may form a novel hybrid gene with new functions (common in cancer).
Dosage effects: Extra or missing gene copies can disturb the balance of gene expression.
Position effects: Moving a gene to a new regulatory environment may silence or over-activate it.

Chromosome Rearrangements in Human Disease

1. Developmental Disorders

Cri-du-chat syndrome: Caused by a deletion on chromosome 5p. Affected infants often have a high-pitched cry and intellectual disability.
Williams syndrome: Results from a microdeletion on chromosome 7q, affecting genes related to cardiovascular and cognitive function.

2. Cancer

Cancer is perhaps the most striking example of disease caused by chromosome rearrangements.

Chronic Myeloid Leukemia (CML): Caused by a translocation between chromosomes 9 and 22, forming the Philadelphia chromosome. This creates the BCR-ABL fusion gene, which drives uncontrolled cell growth.
Burkitt lymphoma: Involves translocation of the MYC gene, leading to excessive cell division.
Ewing sarcoma: A fusion of EWSR1 and FLI1 genes through translocation promotes tumor development.

3. Infertility and Miscarriages

Balanced rearrangements (like inversions or translocations) in carriers may not cause disease directly but can result in:

Recurrent miscarriages
Infertility
Birth defects in offspring

Detecting Rearrangements

Thanks to modern genomics, chromosome rearrangements can now be detected with high precision using:

Karyotyping – Classic method for detecting large rearrangements
FISH (Fluorescence In Situ Hybridization) – Uses fluorescent probes to target specific DNA sequences
Array CGH (Comparative Genomic Hybridization) – Detects copy number changes across the genome
Whole Genome Sequencing (WGS) – Identifies even small or complex rearrangements at base-pair resolution

Looking Forward: The Future of Chromosome Medicine

Understanding chromosome rearrangements is now central to:

Personalized medicine
Genetic counseling
Targeted therapies, especially in cancer (e.g., tyrosine kinase inhibitors for BCR-ABL fusion)

With the rise of long-read sequencing and single-cell genomics, even previously “invisible” rearrangements are being uncovered, offering new insights into both rare diseases and common conditions.

Final Thoughts

Chromosome rearrangements remind us that genetics isn't just about which genes we have — but where they are, how they're arranged, and when they're active. As our tools grow sharper, so does our ability to diagnose, understand, and treat diseases rooted in genomic architecture.

In a way, the genome is like a book not just defined by its words, but also by how the chapters are ordered. Rearranging them can create a new story — sometimes harmful, sometimes insightful — and understanding these changes is key to writing a healthier future.

Phylogenetics

Fri, 23 Aug 2013 03:53:43 -0500

006 - Phylogenetics Paul Andersen discusses the specifics of phylogenetics. The evolutionary relationships of organisms are discovered through both morphological and molecular data. A specific type of phylogenetic tree, the cladogram, is also covered. Intro Music Atribution Title: I4dsong_loop_main.wav Artist: CosmicD Link to sound: http://www.freesound.org/people/CosmicD/sounds/72556/ Creative Commons Atribution License

Mike Ritchie Lab

Wed, 02 Oct 2013 15:25:45 -0500

Mike Ritchie Lab primary research focus is the detection of susceptibility genes for common diseases such as cancer, diabetes, hypertension, and cardiovascular disease, among others. The approaches will involve the development and application of new statistical methods with a focus on the detection of gene-gene interactions associated with human disease.

Gene expression and protein expression patterns between normal and non-normal tissues is a growing area of research that may lead to the identification of candidate genes for understanding the etiology of common, complex diseases.

Lab homepage @ http://ritchielab.psu.edu/ritchielab/

Memories Can Be Passed Down Through DNA

Sat, 10 May 2014 21:24:10 -0500

The premise of Assassin's Creed is the reliving of other people's memories stored inside DNA. Well scientists have found that in mice, it actually happens! Anthony is joined by special guest and our friend Tara Long from Hard Science to explain how this process works, and if it might apply to humans as well. Read More: Parental olfactory experience influences behavior and neural structure in subsequent generations http://www.nature.com/neuro/journal/vaop/ncurrent/abs/nn.3594.html "Using olfactory molecular specificity, we examined the inheritance of parental traumatic exposure, a phenomenon that has been frequently observed, but not understood." What Is Epigenetics? http://www.sciencemag.org/content/330/6004/611 "The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)-genetics." Epigenetics http://en.wikipedia.org/wiki/Epigenetics Watch More: How to Change Your Genes https://www.youtube.com/watch?v=B5DU9lgbsSE TestTube Wild Card http://testtube.com/dnews/dnews-231-how-too-many-screens-affect-our-brain?utm_source=YT&utm_medium=DNews&utm_campaign=DNWC Is Sexiness Hereditary? https://www.youtube.com/watch?v=z6STRCncvM8 ____________________ DNews is dedicated to satisfying your curiosity and to bringing you mind-bending stories & perspectives you won't find anywhere else! New videos twice daily. Watch More DNews on TestTube http://testtube.com/dnews Subscribe now! http://www.youtube.com/subscription_center?add_user=dnewschannel DNews on Twitter http://twitter.com/dnews Anthony Carboni on Twitter http://twitter.com/acarboni Laci Green on Twitter http://twitter.com/gogreen18 Trace Dominguez on Twitter http://twitter.com/trace501 DNews on Facebook http://facebook.com/dnews DNews on Google+ http://gplus.to/dnews Discovery News http://discoverynews.com

National Center for Bioinformatics (NCB)

Wed, 23 Jul 2014 14:10:49 -0500

NCB is offering M.Phil and Ph.D programs in the area of Bioinformatics. The major goal of NCB is to promote quality training and research in the area of Bioinformatics. Bioinformatics originated as a cross-disciplinary field as the need for computational sections to research problem raised in biomedicine.

More at http://ncb.qau.edu.pk/

ChromEvol

Jit — Sun, 25 Jan 2015 00:33:11 -0600

Chromosome number is a remarkably dynamic feature of eukaryotic evolution. Chromosome numbers can change by a duplication of the whole genome (a process termed polyploidy), or by single chromosome changes (ascending dysploidy via, e.g., chromosome fission or descending dysploidy via, e.g., chromosome fusion).
Of the various mechanisms of chromosome number change, polyploidy has received significant attention because of the impact such an event may have on the organism.
ChromEvol implements a series of likelihood models for the evolution of chromosome numbers. By comparing the fit of the different models to biological data, it may be possible to gain insight regarding the pathways by which the evolution of chromosome number proceeds. For each model, the program estimates the rates for the possible transitions assumed by the model, infers the set of ancestral chromosome numbers, and estimates the location along the tree for which polyploidy events (and other chromosome number changes) occurred. For further methodological details, see the publications and manual on the Downloads page.

http://www.tau.ac.il/~itaymay/cp/chromEvol/about.html

Address of the bookmark: http://www.tau.ac.il/~itaymay/cp/chromEvol/downloads.html

Computer simulation of genetic mechanism !!

Jit — Sun, 13 Mar 2016 09:29:56 -0500

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

Simulation models have become important tools in Bioinformatics studies. There are many reasons for this, but we emphasize three of the more important:

(1) they enable exploration of hypotheses, and as such, have become invaluable means to guide research;

(2) they are unique approaches to integrate (in the literal term of the word) biological knowledge, in the form of experimental results; and

(3) they enable connecting biology with other fields of study ranging from physiology to genomics;

This blog, and this software list, is intended to guide the potential user of simulation models.
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.

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.

Software Resource	Brief Description and Homepage
Aladyn	Tools to investigate how demographic parameters, populations genetics and abiotic conditions affect the rate of adaptation http://www.katja-schiffers.eu/research.html
ALF	A Simulation Framework for Genome Evolution http://www.cbrg.ethz.ch/alf
ART	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. http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
BAMSurgeon	Methods for realistic simulation of mutations in real data. https://github.com/adamewing/bamsurgeon
Bayesian Serial SimCoal	Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. http://www.stanford.edu/group/hadlylab/ssc/index.html
BaySICS	An integral platform with a graphical interface for statistical inference based on approximate Bayesian computation. https://sites.google.com/site/baysicsabc/
BEERS	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 http://cbil.upenn.edu/beers/
BOTTLENECK	Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html
BottleSim	BottleSim is a computer simulation program for simulating the process of population bottlenecks http://chkuo.name/software/bottlesim.html
CASS	Protein Sequence Simulation https://liberles.cst.temple.edu/software/cass/index.html
CDPOP	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. http://cel.dbs.umt.edu/cdpop
Classical Genetics Simulator	Web-based simulation software http://www.cgslab.com/
CoaSim	CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. http://users-birc.au.dk/mailund/coasim/index.html
cosi	The cosi package is written in C and is available as a tar file. http://www.broadinstitute.org/~sfs/cosi/
CS-PSeq-Gen	A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen/
DAWG	An application designed to simulate the evolution of recombinant DNA sequences in continuous time http://scit.us/projects/dawg
Easypop	EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions http://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html
EggLib	EggLib is a C++/Python library and program package for evolutionary genetics and genomics. http://egglib.sourceforge.net/
EpiSIM	EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis https://sourceforge.net/projects/episimsimulator/files/
EvolSimulator	A simulation test bed for hypotheses of genome evolution http://acb.qfab.org/acb/evolsim/
EvolveAGene	A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions http://bellinghamresearchinstitute.com/software/index.html
fastsimcoal	A continuous-‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios http://cmpg.unibe.ch/software/fastsimcoal/
FastSLINK	Simulation of Marker and Phenotype Data in Pedigrees https://watson.hgen.pitt.edu/
FFPopSim	C++/Python library for population genetics. http://webdav.tuebingen.mpg.de/ffpopsim/
FLUX SIMULATOR	The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. http://sammeth.net/confluence/display/sim/home
forqs	Forward-in-time simulation of Recombination, Quantitative Traits, and Selection https://bitbucket.org/dkessner/forqs
ForSim	ForSim: A Forward Evolutionary Computer Simulation http://anth.la.psu.edu/research/weiss-lab/research/research
ForwSim	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. http://badri-populationgeneticsimulators.blogspot.com/
FPG	Forward Population Genetic simulation https://bio.cst.temple.edu/~hey/software/software.htm#fpg
FREGENE	FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. http://www.ebi.ac.uk/projects/bargen
FIGG	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 http://insilicogenome.sourceforge.net/
fwdpp	A C++ template library for implementing efficient forward simulations. http://molpopgen.github.io/fwdpp/
GAMETES	Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. http://sourceforge.net/projects/gametes/?source=navbar
GASP	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. http://research.nhgri.nih.gov/gasp/
GCTA	Genome-wide Complex Trait Analysis http://www.complextraitgenomics.com/software/gcta/download.html
GemSIM	Next generation sequencing read simulator http://sourceforge.net/projects/gemsim/
GeneArtisan	Simulation of Markers in Case-Control Study Designs http://www.rannala.org/?page_id=241
GENOME	A rapid coalescent-based whole genome simulator http://www.sph.umich.edu/csg/liang/genome/
GenomePop2	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. https://ritchielab.psu.edu/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla
GenomeSimla	GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested http://chgr.mc.vanderbilt.edu/genomesimla/
GENS2	Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. https://sourceforge.net/projects/gensim/
GWAsimulator	A rapid whole genome simulation program http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator
HAP-SAMPLE	An association simulator for candidate regions or genome scans http://www.hapsample.org/
HAPGEN	A simulator for the simulation of case control datasets at SNP markers https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
HapSim	A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients http://cran.r-project.org/web/packages/hapsim/index.html
HAPSIMU	A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model http://l.web.umkc.edu/liujian/
IBDsim	IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models. http://raphael.leblois.free.fr/
indel-Seq-Gen	A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies http://bioinfolab.unl.edu/~cstrope/isg/
Indelible	A powerful and flexible simulator of biological evolution http://abacus.gene.ucl.ac.uk/software/indelible/
invertFREGENE	InvertFREGENE is a forward-in-time simulator of inversions in population genetic data http://www.ebi.ac.uk/projects/bargen/
kernalPop	A spatially explicit population genetic simulation engine http://cran.r-project.org/src/contrib/archive/kernelpop/
MaCS	Markovian Coalescent Simulator http://www-hsc.usc.edu/~garykche/
Marlin	Marlin provides a user-friendly interface for performing forward-in-time population genetic simulations. http://www.patrickmeirmans.com/software/marlin.html
Mason	A package for the simulation of nucleotide data. http://www.seqan.de/projects/mason/
mbs	modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html
Mendel's Accountant	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 http://mendelsaccount.sourceforge.net/
MetaPopGen	Simulates genetics in large size metapopulations https://sites.google.com/site/marcoandrello/metapopgen
MetaSim	A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets http://ab.inf.uni-tuebingen.de/software/metasim/
mlcoalsim	Multilocus Coalescent Simulations http://code.google.com/p/mlcoalsim-v1/
ms	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. http://home.uchicago.edu/~rhudson1/source/mksamples.html
msHOT	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. http://home.uchicago.edu/~rhudson1/
msms	A coalescent Simlation tool with selection. http://www.mabs.at/ewing/msms/index.shtml
MySSP	A program for the simulation of DNA sequence evolution across a phylogenetic tree http://www.rosenberglab.net/software.html
Nemo	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. http://nemo2.sourceforge.net/
NetRecodon	Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography http://code.google.com/p/netrecodon/
OncoSimulR	BioConductor package for Forward Genetic Simulation of Cancer Progresion with Epistasis https://github.com/rdiaz02/oncosimul
PEDAGOG	Software for simulating eco-evolutionary population dynamics https://bcrc.bio.umass.edu/pedigreesoftware/node/5
phenosim	A tool to add phenotypes to simulated genotypes http://evoplant.uni-hohenheim.de/doku.php?id=software:software
PhyloSim	An R package for the Monte Carlo simulation of sequence evolution http://www.ebi.ac.uk/goldman-srv/phylosim/
pIRS	Profile-based Illumina pair-end reads simulator https://code.google.com/p/pirs/
ProteinEvolver	Simulation of protein evolution along phylogenies under structure-based substitution models http://code.google.com/p/proteinevolver/
QMSim	QTL and Marker Simulator http://www.aps.uoguelph.ca/~msargol/qmsim/
quantiNEMO	An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population http://www2.unil.ch/popgen/softwares/quantinemo/
RECOAL	Simulates new haplotype data from a reference population of haplotypes. ftp://popgen.usc.edu/
Recodon	Coalescent simulation of coding DNA sequences with recombination, migration and demography http://code.google.com/p/recodon/
rlsim	A package for simulating RNA-seq library preparation with parameter estimation http://bit.ly/rlsim-git
Rmetasim	Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R http://cran.r-project.org/web/packages/rmetasim/index.html
RNA Seq Simulator	RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator
Rose	Random model of sequence evolution http://bibiserv.techfak.uni-bielefeld.de/rose/
scrm	A coalescent simulator optimized for long sequences and large samples. https://scrm.github.io/
SelSim	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 http://www.well.ox.ac.uk/~spencer/selsim/
Seq-Gen	An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. http://tree.bio.ed.ac.uk/software/seqgen/
SEQPower	Statistical power analysis for sequence-based association studies http://bioinformatics.org/spower/
SeqSIMLA	SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. http://seqsimla.sourceforge.net/
Serial NetEvolve	A flexible utility for generating serially-sampled sequences along a tree or recombinant network http://biorg.cis.fiu.edu/sne/
SFS_CODE	SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects. http://sfscode.sourceforge.net/sfs_code/index/index.html
SIBSIM	Quantitative phenotype simulation in extended pedigrees http://sourceforge.net/projects/sibsim/
SimAdapt	A spatially explicit, individual-based, forward-time, landscape-genetic simulation model combined with a landscape cellular automaton. https://www.openabm.org/model/3137
SIMCOAL2	A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models http://cmpg.unibe.ch/software/simcoal2/
SimCopy	An R package simulating the evolution of copy number profiles along a tree. http://bit.ly/simcopy
SIMLA	SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies. http://dmpi.duke.edu/simla-simulation-software-version-32
SimPed	A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures http://bioinformatics.org/simped/
Simprot	A program to simulate protein evolution by substitution, insertion and deletion http://www.uhnresearch.ca/labs/tillier/software.htm#3
SimRare	Rare variant simulation and analysis tool http://code.google.com/p/simrare/
simuGWAS	A forward-time simulator that simulates realistic samples for genome-wide association studies. http://simupop.sourceforge.net/cookbook/simugwas
simuPOP	simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. http://simupop.sourceforge.net/
SISSI	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. http://www.cibiv.at/software/sissi/
SMARTPOP	Simulating Mating Alliance as a Reproductive Tactic for Populations http://smartpop.sourceforge.net/
SNPsim	Coalescent simulation of hotspot recombination http://code.google.com/p/phylosoftware/
SPIP	SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user http://swfsc.noaa.gov/textblock.aspx?division=fed&id=3434
Splatche	Spatial and Temporal Coalescences in Heterogeneous Environment http://www.splatche.com/
srv	Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. http://simupop.sourceforge.net/cookbook/simurarevariants
SUP	SLINK/FastSLINK utility program http://mlemire.freeshell.org/software.html
TreesimJ	A flexible, forward-time population genetic simulator http://code.google.com/p/treesimj/
Variant Simulation Tools	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. http://varianttools.sourceforge.net/simulation/homepage
Vortex	VORTEX is an individual-based simulation model for population viability analysis (PVA). http://www.vortex9.org/vortex.html
Wessim	Whole Exome Sequencing SIMulator http://sak042.github.io/wessim/