StarGenetics – Mendelian Genetics Cross Simulator

StarGenetics

:: DESCRIPTION

StarGenetics is a Mendelian genetics cross simulator. StarGenetics allows students to simulate mating experiments between organisms that are genetically different across a range of traits to analyze the nature of the traits in question. Its goal is to teach students about genetic experimental design and genetic concepts.

:: DEVELOPER

The STAR program at MIT

:: SCREENSHOTS

StarGenetics

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 StarGenetics

:: MORE INFORMATION

Ped-sim v1.3.5 – Pedigree Simulator

Ped-sim v1.3.5

:: DESCRIPTION

Ped-sim enables simulations of data for individuals from a given pedigree structure. It can use sex-specific genetic maps to incorporate differences in male and female recombination events.

::DEVELOPER

Williams lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Ped-sim

:: MORE INFORMATION

Citation:

Caballero M, Seidman DN, Qiao Y, Sannerud J, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Carmi S, Williams AL.
Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives.
PLoS Genet. 2019 Dec 20;15(12):e1007979. doi: 10.1371/journal.pgen.1007979. PMID: 31860654; PMCID: PMC6944377.

PBSIM 1.0.3 – PacBio Reads Simulator

PBSIM 1.0.3

:: DESCRIPTION

PacBio sequencers produced two types of characteristic reads: CCS (short and low error rate) and CLR (long and high error rate), both of which could be useful for de novo assembly of genomes. PBSIM simulates those PacBio reads by using either a model-based or sampling-based simulation.

::DEVELOPER

Yukiteru Ono ,Kiyoshi Asai ,Michiaki Hamada 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PBSIM

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jan 1;29(1):119-21. doi: 10.1093/bioinformatics/bts649.
PBSIM: PacBio reads simulator–toward accurate genome assembly.
Ono Y, Asai K, Hamada M.

QMSIM 1.10 – Qtl and Marker SIMulator

QMSIM 1.10

:: DESCRIPTION

QMSim (Qtl and Marker SIMulator) was designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data.

::DEVELOPER

Mehdi Sargolzaei , Flavio Schenkel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 QMSim

:: MORE INFORMATION

Citation

Sargolzaei, M. and F. S. Schenkel. 2009.
QMSim: a large-scale genome simulator for livestock.
Bioinformatics, 25: 680-681. doi:10.1093 /bioinformatics/btp045

SCRIP 1.0.0 – An Accurate Simulator for Single-Cell RNA Sequencing Data

SCRIP 1.0.0

:: DESCRIPTION

SCRIP provides a flexible Gamma-Poisson mixture and a Beta-Gamma-Poisson mixture framework to simulate scRNA-seq data.

::DEVELOPER

Fei Qin [aut, cre, cph]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

SCRIP

:: MORE INFORMATION

Citation:

Qin F, Luo X, Xiao F, Cai G.
SCRIP: an accurate simulator for single-cell RNA sequencing data.
Bioinformatics. 2021 Dec 7:btab824. doi: 10.1093/bioinformatics/btab824. Epub ahead of print. PMID: 34874992.

CellLine – Stochastic Cell Lineage Simulator

CellLine

:: DESCRIPTION

CellLine is a simulator of the dynamics of gene regulatory networks (GRN) in the cells of a lineage. From user-defined reactions and initial substance quantities, it generates cell lineages, i.e. genealogic pedigrees of cells related through mitotic division. Each cell’s dynamics is driven by a delayed stochastic simulation algorithm (delayed SSA), allowing multiple time delayed reactions.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CellLine

:: MORE INFORMATION

Citation:

Andre S. Ribeiro, Daniel A. Charlebois, Jason Lloyd-Price,
CellLine, a stochastic cell lineage simulator“,
Bioinformatics, (accepted), Sept. 2007.

SGN Sim / SGNS2 2.1.170 – Stochastic Genetic Networks Simulator

SGN Sim / SGNS2 2.1.170

:: DESCRIPTION

SGNSim (Stochastic Gene Networks Simulator) is a tool to model gene regulatory networks (GRN) where transcription and translation are modeled as multiple time delayed events and its dynamics is driven by a stochastic simulation algorithm (SSA) able to deal with multiple time delayed events. The delays can be drawn from several distributions and the reaction rates from complex functions or from physical parameters. SGNSim can generate ensembles of GRNs, within a set of user-defined parameters, such as topology. It can also be used to model specific GRNs and systems of chemical reactions. Perturbations, e.g. gene deletion, over-expression, copy and mutation, can be modeled as well.

  • SGNS2 (Simulator of delayed stochastic genetic circuits. Version 2, which includes transient compartmentalization of reactions)

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SGN Sim / SGNS2

:: MORE INFORMATION

Citation:

Lloyd-Price J, Gupta A, Ribeiro AS.
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations.
Bioinformatics. 2012 Nov 15;28(22):3004-5. doi: 10.1093/bioinformatics/bts556. Epub 2012 Sep 26. PMID: 23014631.

Andre S. Ribeiro; Jason Lloyd-Price, (2007)
SGN Sim, a Stochastic Genetic Networks Simulator
Bioinformatics, 23(6):777-779. doi:10.1093/bioinformatics/btm004.

AdmixSim 2.0 – Forward-time Simulator of Population Genetic data

AdmixSim 2.0

:: DESCRIPTION

AdmixSim is an individual-based forward-time simulation tool that can flexibly and efficiently simulate population genomics data under complex evolutionary scenarios. It is based on the extended Wright-Fisher model, and it implements many common evolutionary parameters to involve gene flow, natural selection, recombination, and mutation.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

AdmixSim

:: MORE INFORMATION

Citation

Zhang R, Liu C, Yuan K, Ni X, Pan Y, Xu S.
AdmixSim 2: a forward-time simulator for modeling complex population admixture.
BMC Bioinformatics. 2021 Oct 18;22(1):506. doi: 10.1186/s12859-021-04415-x. PMID: 34663213; PMCID: PMC8522168.

Hapsample 0.12 – Association Simulator for Candidate Regions or Genome Scans

Hapsample 0.12

:: DESCRIPTION

HAP-SAMPLE is an application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be “genotyped,” along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans.

::DEVELOPER

Fei Zou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

Hapsample

:: MORE INFORMATION

Citation

Wright, F.A, Huang, H., Guan, X., Gamiel, K, Jeffries, C., Barry, W.T., de Villena, F.P., Sullivan, P.F., Wilhelmsen, K.C., and Zou. F. (2007)
Simulating association studies: a data-based resampling method for candidate regions or whole genome scans,
Bioinformatics 23: 2581-2588.

MESA – MOSLA Error Simulator

MESA

:: DESCRIPTION

MESA is a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms.

::DEVELOPER

Distributed Systems and Intelligent Computing

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MESA

:: MORE INFORMATION

Citation

Schwarz M, Welzel M, Kabdullayeva T, Becker A, Freisleben B, Heider D.
MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors.
Bioinformatics. 2020 Jun 1;36(11):3322-3326. doi: 10.1093/bioinformatics/btaa140. PMID: 32129840; PMCID: PMC7267826.

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