AnA-FiTS 1.0.3 – Forward-in-time Simulator for Polymorphism data

AnA-FiTS 1.0.3

:: DESCRIPTION

AnA-FiTS is an efficient tool for simulating polymorphism data forward-in-time on the chromosome and genome level.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD 

  AnA-FiTS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Jul 9;14:216. doi: 10.1186/1471-2105-14-216.
Rapid forward-in-time simulation at the chromosome and genome level.
Aberer AJ, Stamatakis A.

RNASeqReadSimulator – A Simple RNA-Seq Read Simulator

RNASeqReadSimulator

:: DESCRIPTION

RNASeqReadSimulator is a set of scripts generating simulated RNA-Seq reads. RNASeqReadSimulator provides users a simple tool to generate RNA-Seq reads for research purposes, and a framework to allow experienced users to expand functions.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

  RNASeqReadSimulator

:: MORE INFORMATION

BEnDS – Binding Energy Distribution Simulator

BEnDS

:: DESCRIPTION

BEnDS can generate random binding energy matrices and simulate binding probabilities of DNA sequences.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

BEnDS

:: MORE INFORMATION

Citation

Ruan S, Stormo GD.
Inherent limitations of probabilistic models for protein-DNA binding specificity.
PLoS Comput Biol. 2017 Jul 7;13(7):e1005638. doi: 10.1371/journal.pcbi.1005638

ShotGun 1.0.10 – Flexible Short Read Simulator

ShotGun 1.0.10

:: DESCRIPTION

ShotGun is a flexible short read simulator. ShotGun generates sequence data with user-specified read length and average depth, accommodates to cycle specific sequencing error rates, allows the read depth distribution to be either the ideal Poisson or Negative Binomial to model the overdispersion observed with real sequencing data. In addition, ShotGun performs computationally efficient Single Nucleotide Polymorphism (SNP) discovery using a statistic aggregated across all sequenced samples. False positives can be controlled at any desired rate according to the null distribution of this multi-sample statistic.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 ShotGun

:: MORE INFORMATION

TreesimJ 0.7 – Population Genetics Simulator Program

TreesimJ 0.7

:: DESCRIPTION

TreesimJ is a flexible, individual-based population genetic simulator. It tracks the state of a population evolving in forward time via discrete, Wright-Fisher generations.   It also maintains the full genealogical tree of the population and allows for collecting sample trees which can be analyzed, exported and logged.  It can also simulate evolving DNA under a variety of assumptions regarding mutation and selection. TreesimJ is very flexible, meaning that a wide variety of fitness models, demographic models, and data collectors are supported, and new models are easy to write.  The application also sports an intuitive graphical interface, so users unfamiliar with the command line or XML can easily use the program to generate and analyze genetic data.

::DEVELOPER

Brendan O’Fallon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

TreesimJ

:: MORE INFORMATION

Citation:

Brendan O’Fallon
TreesimJ: a flexible, forward time population genetic simulator
Bioinformatics (2010) 26 (17): 2200-2201

IntSIM – An Integrated Simulator of Next-Generation Sequencing Data

IntSIM

:: DESCRIPTION

The IntSim software package has been developed to simulate various genome mutations including germline and somatic variations from next generation sequencing data, and also to generate read data from mixed genomes by considering moderate levels of tumor purity.

::DEVELOPER

IntSIM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 IntSIM

:: MORE INFORMATION

Citation

IntSIM: An Integrated Simulator of Next-Generation Sequencing Data.
Yuan X, Zhang J, Yang L.
IEEE Trans Biomed Eng. 2016 Apr 29.

DSD 20160312 – DNA Strand Displacement Simulator

DSD 20160312

:: DESCRIPTION

DSD is a new programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism.

::DEVELOPER

Matthew Lakin,  Filippo Polo, Simon Youssef, Kathryn Gray, Rasmus Petersen, Luca Cardelliand Andrew Phillips.

:: SCREENSHOTS

dsd

:: REQUIREMENTS

:: DOWNLOAD

 DSD

:: MORE INFORMATION

Citation

Visual DSD: a design and analysis tool for DNA strand displacement systems.
Lakin MR, Youssef S, Polo F, Emmott S, Phillips A.
Bioinformatics. 2011 Nov 15;27(22):3211-3. doi: 10.1093/bioinformatics/btr543

scrm 1.7.2 – Coalescent Simulator for Biological Sequences

scrm 1.7.2

:: DESCRIPTION

scrm (sequential coalescent with recombination model ) is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage.

::DEVELOPER

scrm team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 scrm

:: MORE INFORMATION

Citation

scrm: efficiently simulating long sequences using the approximated coalescent with recombination.
Staab PR, Zhu S, Metzler D, Lunter G.
Bioinformatics. 2015 Jan 8. pii: btu861

MSAcquisitionSimulator 1.0.2 – Data-dependent Acquisition Simulator for LC-MS Shotgun Proteomics

MSAcquisitionSimulator 1.0.2

:: DESCRIPTION

MSAcquisitionSimulator is a collection of three command-line tools that simulate data-dependent acquisition algorithms on in silico generated ground truth data of liquid chromatography-mass spectrometry proteomics experiments.

::DEVELOPER

Major Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MSAcquisitionSimulator

:: MORE INFORMATION

Citation

MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics.
Goldfarb D, Wang W, Major MB.
Bioinformatics. 2015 Dec 17. pii: btv745.

SimPhy 1.0.1 – A comprehensive Simulator of Gene Family Evolution

SimPhy 1.0.1

:: DESCRIPTION

SimPhy is a program for the simulation of gene family evolution under incomplete lineage sorting (ILS), gene duplication and loss (GDL), replacing horizontal gene transfer (HGT) and gene conversion (GC).

::DEVELOPER

Phylogenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux

:: DOWNLOAD

 SimPhy

:: MORE INFORMATION

Citation

SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees.
Mallo D, de Oliveira Martins L, Posada D.
Syst Biol. 2015 Nov 1. pii: syv082.