<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34400? https://bioinformaticsonline.com/blog/view/34916/bioinformatics-tools-developed-for-oxford-nanopore-data-analysis Wed, 27 Dec 2017 20:47:30 -0600 https://bioinformaticsonline.com/blog/view/34916/bioinformatics-tools-developed-for-oxford-nanopore-data-analysis <![CDATA[Bioinformatics tools developed for Oxford Nanopore data analysis !]]> MinION is the only portable real-time device for DNA and RNA sequencing. Each consumable flow cell can now generate 10–20 Gb of DNA sequence data. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length. One of the technical advantages of ONT data is the read length, which offers great prospects for genome assembly. Generally, assemblers are based on several different types of algorithms, such as greedy, overlap-layout-consensus (OLC), de Bruijn graph (DBG), and string graph.

List of analysis tools developed for Oxford Nanopore data

BWA
Fast nanopore data tuned alignment tool
https://github.com/lh3/bwa

GraphMap
Mapper for long and error-prone reads
https://github.com/isovic/graphmap

LAST
Nanopore tuned alignment tool
http://last.cbrc.jp/

LINKS
Software tool for long read scaffolding
https://github.com/warrenlr/LINKS/

marginAlign
Tools to align nanopore reads to a reference
https://github.com/benedictpaten/marginAlign

minoTour
Real time analysis tools
http://minotour.nottingham.ac.uk/

nanoCORR
Error-correction tool for nanopore sequence data
https://github.com/jgurtowski/nanocorr

NanoOK
Software for nanopore data, quality and error profiles
https://documentation.tgac.ac.uk/display/NANOOK/NanoOK

Nanopolish
Nanopore analysis and genome assembly software
https://github.com/jts/nanopolish

nanopore
Variant-detection tool for nanopore sequence data
https://github.com/mitenjain/nanopore

Nanocorrect
Error-correction tool for nanopore sequence data
https://github.com/jts/nanocorrect/

npReader
Real-time conversion and analysis of nanopore reads
https://github.com/mdcao/npReader

poRe
Tool for analyzing and visualizing nanopore data
https://sourceforge.net/p/rpore/wiki/Home/

PoreSeq
Error-correction and variant-calling software
https://github.com/tszalay/poreseq

Poretools
Nanopore sequence analysis and visualization software
https://github.com/arq5x/poretools

SSPACE-LongRead
Genome scaffolding tool
http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread

SMIS
Genome scaffolding tool
https://sourceforge.net/projects/phusion2/files/smis/

 

List of assemblers for Oxford Nanopore MinION long reads

LQS
DALIGNER, Celera OLC Nanocorrect,
Nanopolish corrector
https://github.com/jts/nanopolish

PBcR
HGAP or BLASR, Celera OLC
PBcR corrector
http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR
–
Canu
MHAP, Celera OLC
Canu corrector
https://github.com/marbl/canu

Falcon
String graph, Celera OLC
Falcon corrector
https://github.com/PacificBiosciences/falcon

Miniasm
OLC
https://github.com/lh3/miniasm

ra-integrate
OLC
https://github.com/mariokostelac/ra-integrate/

ALLPATHS-LG
de Bruijn graph
ALLPATHS-L corrector
https://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12

SPAdes
de Bruijn graph
SPAdes corrector
http://bioinf.spbau.ru/spades

]]> biogeek https://bioinformaticsonline.com/poll/view/23590/will-minion-nanopore-sequencing-increase-the-number-of-next-generation-sequencing-projects Tue, 04 Aug 2015 05:14:07 -0500 https://bioinformaticsonline.com/poll/view/23590/will-minion-nanopore-sequencing-increase-the-number-of-next-generation-sequencing-projects <![CDATA[Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?]]> Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?

]]> Strand https://bioinformaticsonline.com/bookmarks/view/33660/equant-energy-based-quality-assessment-of-protein Sat, 24 Jun 2017 19:24:24 -0500 https://bioinformaticsonline.com/bookmarks/view/33660/equant-energy-based-quality-assessment-of-protein <![CDATA[eQuant : energy-based quality assessment of protein]]> Protein structures are of varying quality. Especially, in-silico modeled structures are prone to contain serious errors, which limit the usefulness and reliability of these particular protein structures.

eQuant is a service for structure quality assessment of single proteins, which utilizes a coarse-grained energy model. The overall quality is calculated as well as the reliability of individual residues. You can submit single PDB files or archives containing a set of proteins.

https://biosciences.hs-mittweida.de/equant/

Address of the bookmark: https://biosciences.hs-mittweida.de/equant/

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/44476/omark-software-for-proteome-protein-coding-gene-repertoire-quality-assessment Wed, 21 Feb 2024 15:01:20 -0600 https://bioinformaticsonline.com/bookmarks/view/44476/omark-software-for-proteome-protein-coding-gene-repertoire-quality-assessment <![CDATA[OMArk: software for proteome (protein-coding gene repertoire) quality assessment]]> OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families.

Address of the bookmark: https://github.com/DessimozLab/OMArk

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/34504/minion-gc-an-r-script-to-do-some-qc-on-minion-data Sun, 03 Dec 2017 15:19:18 -0600 https://bioinformaticsonline.com/bookmarks/view/34504/minion-gc-an-r-script-to-do-some-qc-on-minion-data <![CDATA[MinION_GC: An R script to do some QC on MinION data]]> Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out there: it takes about a minute to analyse a 4GB flowcell on my laptop.

https://github.com/roblanf/minion_qc

Address of the bookmark: https://github.com/roblanf/minion_qc

]]> Radha Agarkar https://bioinformaticsonline.com/bookmarks/view/34475/oxford-nanopore-sequencing-hybrid-error-correction-and-de-novo-assembly-of-a-eukaryotic-genome Wed, 29 Nov 2017 05:08:53 -0600 https://bioinformaticsonline.com/bookmarks/view/34475/oxford-nanopore-sequencing-hybrid-error-correction-and-de-novo-assembly-of-a-eukaryotic-genome <![CDATA[Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome]]> Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.

Address of the bookmark: http://schatzlab.cshl.edu/data/nanocorr/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data Tue, 22 Jan 2019 06:26:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data <![CDATA[Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data]]>
  • Run a pipeline processing fast5s to a consensus in a single command.
  • Recommended fixed "standard" and "fast" pipelines.
  • Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
  • Seemless distribution of tasks over local or distributed compute.
  • Highly configurable.
  • Open source (Mozilla Public License 2.0).

    • Documentation can be found at https://nanoporetech.github.io/katuali/.

    Address of the bookmark: https://github.com/nanoporetech/katuali

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data Thu, 23 Nov 2017 09:55:57 -0600 https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data <![CDATA[poRe: an R package for the visualization and analysis of nanopore sequencing data]]> Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

    Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

    Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

    Contact:mick.watson@roslin.ed.ac.uk

    Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/1/114/2365693

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/28141/csbb-v10 Wed, 29 Jun 2016 07:33:05 -0500 https://bioinformaticsonline.com/bookmarks/view/28141/csbb-v10 <![CDATA[CSBB-v1.0]]> CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R and python in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX, MAC OS and Windows platforms.

    Currently CSBB provides 13 modules focused on analytical tasks like performing upper-quantile normalization on expression data or convert genome wide gene expression to z-scores when comparing expression data from different platforms.

    More at https://github.com/skygenomics/CSBB-v1.0

    Address of the bookmark: https://github.com/skygenomics/CSBB-v1.0

    ]]>     Neel     https://bioinformaticsonline.com/pages/view/8265/list-of-generic-simulation-softwaretoolsresource-with-brief-description-and-homepage Mon, 10 Feb 2014 05:57:29 -0600 https://bioinformaticsonline.com/pages/view/8265/list-of-generic-simulation-softwaretoolsresource-with-brief-description-and-homepage <![CDATA[List of generic simulation software/tools/resource with brief description and homepage !!!]]> List of generic simulation software/tools/resource with brief description and homepage

    image

    ALF
    A Simulation Framework for Genome Evolution
    http://www.cbrg.ethz.ch/alf

    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

    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
    http://www.wyomingbioinformatics.org/liberlesgroup/cass/

    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

    CoalFace
    CoalFace is a simulation of the coalescent process with the visual display of gene genealogies.
    http://web.up.ac.za/default.asp?ipkcategoryid=3283

    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.html

    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/page36926_fr.html

    EggLib
    EggLib is a C++/Python library and program package for evolutionary genetics and genomics.
    http://egglib.sourceforge.net/

    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
    http://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://flux.sammeth.net/simulator.html

    ForSim
    ForSim: A Forward Evolutionary Computer Simulation
    http://www.anthro.psu.edu/weiss_lab/research.shtml

    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
    http://genfaculty.rutgers.edu/hey/software#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/download/fregen/documentation_html.html

    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/

    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.
    http://webs.uvigo.es/acraaj/genomepop2.htm

    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/

    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/

    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.php

    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/

    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://bit.ly/rlsim-git

    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://linum.cofc.edu/software.html#metasim

    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/

    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/

    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://www.chg.duke.edu/research/simla.html

    SimPed
    A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures
    http://www.hgsc.bcm.tmc.edu/content/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/simucomplexdisease

    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/

    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/

    Vortex
    VORTEX is an individual-based simulation model for population viability analysis (PVA).
    http://www.vortex9.org/vortex.html

    References:

    Image www.evolution-of-life.com

    www.cancer.gov

    ]]>     Jit