TESD 1.0 – Transposable Element Simulator Dynamics

TESD 1.0

:: DESCRIPTION

TESD simulates the number of genomic TE copies in different populations across generations (according to the Island Model), using classical models of TE dynamics. The parameters of the models (transposition and excision rates, selection intensity, recombination rate, migration rate, population sizes and number of populations) are defined by the users.

::DEVELOPER

TESD team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • Java

:: DOWNLOAD

  TESD

:: MORE INFORMATION

Citation:

Grégory Deceliere, Yann Letrillard, Sandrine Charles and Christian Biémont
TESD: a transposable element dynamics simulation environment
Bioinformatics November 1, 2006 22:2702-2703

NFsim 1.11 – Biochemical Reaction Simulator

NFsim 1.11

:: DESCRIPTION

NFsim (Network Free Stochastic Simuloator) is a free, open-source, biochemical reaction simulator designed to handle systems that have a large or even infinite number of possible molecular interactions or states. NFsim also has advanced and flexible options for simulating coarse-grained representations of complex nonlinear reaction mechanisms.

NFsim is ideal for modeling polymerization, aggregation, and cooperative reactions that cannot be handled with traditional stochastic or ODE simulators. Models are specified in the BioNetGen Langauge, providing a powerful model building environment.

::DEVELOPER

the Emonet lab at Yale University and the Faeder lab at the University of Pittsburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

NFsim

:: MORE INFORMATION

Citation:

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim.
Sneddon MW, Faeder JR, Emonet T.
Nat Methods. 2011 Feb;8(2):177-83. doi: 10.1038/nmeth.1546.

SVEngine – Allele Specific and Haplotype Aware Structural Variants Simulator

SVEngine

:: DESCRIPTION

SVEngine (Structural Variants Engine) is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

SVEngine

:: MORE INFORMATION

Citation

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy081.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.
Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP

PaSS – A PacBio Sequencing Simulator

PaSS

:: DESCRIPTION

PaSS is a fast sequencing simulator for PacBio sequencing with a high fidelity. It will facilitate the evaluation and development of new analysis tools for the PacBio sequencing data.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

PaSS

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2019 Jun 21;20(1):352. doi: 10.1186/s12859-019-2901-7.
PaSS: a sequencing simulator for PacBio sequencing.
Zhang W, Jia B, Wei C

NeSSM / NeSSMt – Next-generation Sequencing Simulator for Metagenomics / Metatranscriptomics

NeSSM / NeSSMt

:: DESCRIPTION

NeSSM is a tool to generate Next-Generation Sequencing (NGS) reads with parameters set by users. The goal of NeSSM is to generate metagenome sequencing reads close to the reality.

NeSSMt is a metatranscriptome simulator. Using a composition table and reference transcripts or genomes (with annotation file)

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  NeSSM / NeSSMt

:: MORE INFORMATION

Citation:

PLoS One. 2013 Oct 4;8(10):e75448. doi: 10.1371/journal.pone.0075448. eCollection 2013.
NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
Jia B1, Xuan L, Cai K, Hu Z, Ma L, Wei C.

myPresto 5.000 / omegagene 0.38 – Medicinally Yielding PRotein Engineering SimulaTOr

myPresto 5.000 / omegagene 0.38

:: DESCRIPTION

myPresto is a program suite composed of several molecular simulations for drug development.

myPresto/omegagene is a Molecular Dynamics Simulation Engine.

::DEVELOPER

myPresto team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
:: DOWNLOAD

myPresto

:: MORE INFORMATION

Citation

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.
Kasahara K, Ma B, Goto K, Dasgupta B, Higo J, Fukuda I, Mashimo T, Akiyama Y, Nakamura H.
Biophys Physicobiol. 2016 Sep 7;13:209-216.

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