simNGS 20130502 – Simulate Observations from Illumina NGS machines

simNGS 20130502

:: DESCRIPTION

simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be present in real data (“dust”, bubbles, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 simNGS

:: MORE INFORMATION

SimulaTE 1.13 – Simulating Complex Landscapes of Transposable Elements of Populations

SimulaTE 1.13

:: DESCRIPTION

SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.

::DEVELOPER

Institute of Population Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

SimulaTE

:: MORE INFORMATION

Citation:

SimulaTE: simulating complex landscapes of transposable elements of populations.
Kofler R.
Bioinformatics. 2018 Apr 15;34(8):1419-1420. doi: 10.1093/bioinformatics/btx772.

Seq-Gen 1.3.4 – Simulate the Evolution of Sequences along a Phylogeny

Seq-Gen 1.3.4

:: DESCRIPTION

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Seq-Gen

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Jun;13(3):235-8.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
Rambaut A1, Grassly NC.

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,

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.

polyester 1.6.0 – Simulate RNA-seq Reads

polyester 1.6.0

:: 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.

Pyvolve 0.7.2 – Python Library to Simulate Evolutionary Sequence data

Pyvolve 0.7.2

:: DESCRIPTION

Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution.

::DEVELOPER

Stephanie J. Spielman @Claus Wilke’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pyvolve

:: MORE INFORMATION

Citation

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.
Spielman SJ, Wilke CO.
PLoS One. 2015 Sep 23;10(9):e0139047. doi: 10.1371/journal.pone.0139047.

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

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.

RateEvolver 1.1 – Simulate Evolution of Substitution Rate on Fixed Nine-taxon Tree

RateEvolver 1.1

:: DESCRIPTION

RateEvolver simulates the evolution of the substitution rate on a fixed nine-taxon tree. It allows the rate to vary among branches in either an autocorrelated or uncorrelated manner.

::DEVELOPER

the Molecular Ecology, Evolution, and Phylogenetics laboratory in the School of Biological Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 RateEvolver

:: MORE INFORMATION

Citation

Ho, S. Y., Phillips, M. J., Drummond, A. J., & Cooper, A. (2005).
Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation.
Molecular Biology and Evolution, 22(5), 1355-1363.