AlleleRetain 2.0.2 – Simulate Small Populations

AlleleRetain 2.0.2

:: DESCRIPTION

AlleleRetain is a package implemented in R to simulate small populations.  Output includes demographic trends and information, probability of retaining a rare allele, and accumulation of inbreeding over the simulated period.

::DEVELOPER

AlleleRetain team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

  AlleleRetain

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2012 Nov;12(6):1161-7. doi: 10.1111/j.1755-0998.2012.03176.x. Epub 2012 Aug 27.
AlleleRetain: a program to assess management options for conserving allelic diversity in small, isolated populations.
Weiser EL1, Grueber CE, Jamieson IG.

SIMLD 1.0 – Simulate Linkage Disequilibrium

SIMLD 1.0

:: DESCRIPTION

SIMLD is a software package to simulate realistic linkage disequilibrium patterns based on HapMap data

::DEVELOPER

Xiguo Yuan 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SIMLD

:: MORE INFORMATION

Citation

Biochem Genet. 2011 Jun;49(5-6):395-409. doi: 10.1007/s10528-011-9416-x. Epub 2011 Jan 14.
Simulating linkage disequilibrium structures in a human population for SNP association studies.
Yuan X1, Zhang J, Wang Y.

Coancestry 1.0.1.2 – Simulate, Estimate and Analyse Relatedness and Inbreeding Coefficients

Coancestry 1.0.1.2

:: DESCRIPTION

COANCESTRY is a computer program that implements 7 methods to estimate the pairwise relatedness between individuals and 4 methods to estimate individual inbreeding coefficients, using individual genotypes at a set of marker loci.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

Coancestry

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Coancestry

:: MORE INFORMATION

Citation

COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients.
Wang J.
Mol Ecol Resour. 2011 Jan;11(1):141-5. doi: 10.1111/j.1755-0998.2010.02885.x.

TranscriptSimulator 0.7 – Simulate Transcriptome Next-gen Reads, including 454 and Illumina

TranscriptSimulator 0.7

:: DESCRIPTION

TranscriptSimulator: Simple text-based, next-gen output simulator. Specifically designed to simulate transcriptome next-gen reads, including 454 and Illumina. Uses a model to simulate transcription followed by simulated sequencing using various customizable parameters. Uses a nucleotide gene set as a template (e.g. in silico predicted gene set). Version 0.70 has simulated SNPs/Indels with an improved model.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 TranscriptSimulator

:: MORE INFORMATION

NU-IN 1.0.3 – Simulate Gene and Genome Evolution

NU-IN 1.0.3

:: DESCRIPTION

The NU-IN extension module is a extension to EvolSimulator. With the NU-IN module, users are now able to simulate both drift and selection at the nucleotide, amino acid, copy number, and gene family levels across sets of related genomes, for user-specified starting sequences and associated parameters.

::DEVELOPER

The Dlugosch Lab @ The University of Arizona

:: SCREENSHOTS

N/A

: REQUIREMENTS

:: DOWNLOAD

 NU-IN

:: MORE INFORMATION

Citation

BMC Res Notes. 2010 Aug 2;3:217. doi: 10.1186/1756-0500-3-217.
NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform.
Dlugosch KM, Barker MS, Rieseberg LH.

EasyPop 2.0.1 – Simulate Population Genetics Datasets

EasyPop 2.0.1

:: DESCRIPTION

EASYPOP is a computer program allowing to simulate population genetics datasets. It allows generating genetic data for haploid, diploid, and haplodiploid organisms under a variety of mating systems. It includes various migration and mutation models. Output can be generated for the FSTAT, GENEPOP, and ARLEQUIN genetic analysis packages.

::DEVELOPER

Francois Balloux (email: fb255@gen.cam.ac.uk)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux / Windows

:: DOWNLOAD

 EASYPOP

:: MORE INFORMATION

Citation

Balloux F.
EASYPOP (version 1.7): a computer program for population genetics simulations.
J Hered. 2001 May-Jun;92(3):301-2.

GENOSIM v4 – Simulate Genotypes, Breeding Values, and Phenotypes

GENOSIM v4

:: DESCRIPTION

GENOSIM is a set of programs to simulate genotypes, breeding values, phenotypes, and DNA sequence read depth and to resolve SNP conflicts between parent and offspring genotypes

::DEVELOPER

Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortron

:: DOWNLOAD

  GENOSIM

:: MORE INFORMATION

polyester 1.28.0 – Simulate RNA-seq Reads

polyester 1.28.0

:: DESCRIPTION

Polyester is an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads

::DEVELOPER

Alyssa Frazee <alyssa.frazee at gmail.com>, Jeff Leek <jtleek at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 Polyester

:: MORE INFORMATION

Citation:

Polyester: simulating RNA-seq datasets with differential transcript expression.
Frazee AC, Jaffe AE, Langmead B, Leek JT.
Bioinformatics. 2015 Apr 28. pii: btv272.

invertFREGENE – Simulate Sequence Level data with Inversions

invertFREGENE

:: DESCRIPTION

invertFREGENE is a software for simulating sequence level data with inversions

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • C Compiler

:: DOWNLOAD

 invertFREGENE

:: MORE INFORMATION

Citation

Paul F. O’Reilly, Lachlan J. M. Coin and Clive J. Hoggart
invertFREGENE: software for simulating inversions in population genetic data
Bioinformatics (2010) 26 (6): 838-840.