Tag: Simulate

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

:: 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.

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.

simMSG – Simulate Accuracy of MSG for your Genome

simMSG

:: DESCRIPTION

SimMSG allows users to simulate hybrids from crossing two parental genomes, and run the MSG (Multiplexed Shotgun Genotyping) pipeline on these simulated hybrids to test the accuracy of the algorithm. It allows researchers to decide on various parameters before they conduct an MSG experiment.

::DEVELOPER

Ray Cui

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SimMSG

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2015 May 28. doi: 10.1111/1755-0998.12434.
simMSG: an experimental design tool for high-throughput genotyping of hybrids.
Schumer M, Cui R, Rosenthal GG, Andolfatto P,

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