GenomeSmasher 1.0 – Creating Artificial Genomes for Next-gen Sequencing Simulations

GenomeSmasher 1.0

:: DESCRIPTION

GenomeSmasher is a set of tools used to create diploid FASTA files with containing snps, indels, duplications, deletions and translocations. These FASTA files can then be used in conjunction with next-generation sequencing simulators to artificially create sequencing experiments. The utility of these tools are to assess the performance and reliability of data analysis in next-generation sequencing pipelines.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 GenomeSmasher

:: MORE INFORMATION

Gargammel – Simulation of ancient DNA sequence data

Gargammel

:: DESCRIPTION

gargammel is a set of programs aimed at simulating ancient DNA fragments. For ancient hominin samples our program can also simulate various levels of present-day human contamination and microbial contamination.

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

gargammel

:: MORE INFORMATION

Citation

Renaud G, Hanghoj K, Willerslev E, Orlando L.
gargammel: a sequence simulator for ancient DNA.
Bioinformatics. 2017 Feb 15;33(4):577-579. doi: 10.1093/bioinformatics/btw670. PMID: 27794556; PMCID: PMC5408798.

SysGenSim 1.2 – Simulation software for Systems Genetics

SysGenSim 1.2

:: DESCRIPTION

SysGenSIM is a bioinformatics toolbox for MATLAB to create artificial gene expression datasets by simulating Systems Genetics experiments.

::DEVELOPER

CRS4-Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 SysGenSIM

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2459-62. doi: 10.1093/bioinformatics/btr407. Epub 2011 Jul 6.
Simulating systems genetics data with SysGenSIM.
Pinna A1, Soranzo N, Hoeschele I, de la Fuente A.

DL_POLY 4 v5.0.0 – Molecular Dynamics Simulations

DL_POLY 4 v5.0.0

:: DESCRIPTION

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software.

::DEVELOPER

DL_POLY team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 DL_POLY

:: MORE INFORMATION

Citation

Philos Trans A Math Phys Eng Sci. 2004 Sep 15;362(1822):1835-52.
DL_POLY_3: the CCP5 national UK code for molecular-dynamics simulations.
Todorov IT1, Smith W.

Populus 6.0 – Simulation software for Population Biology and Evolutionary Ecology

Populus 6.0

:: DESCRIPTION

The Populus software contains a set of simulations that we use to teach population biology and evolutionary ecology at the University of Minnesota. Simulation models may be chosen from a menu, and students can move among the parameter boxes of an input window, changing initial defaults to values of their own choosing.

::DEVELOPER

Populus team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 Populus

:: MORE INFORMATION

Alfacinha – Simulation of Sequence Evolution with Neighbouring-site Dependencies

Alfacinha

:: DESCRIPTION

alfacinha is a source-package of object-oriented Python modules for sequence evolution allowing for neighbor-dependent substitutions under GPL license.This package is aimed at simulating the evolution of sequences along phylogenetic trees. It provides several modules to store and manipulate evolutionary models, to store and evolve a sequence, and store and manipulate evolutionary trees

::DEVELOPER

Leonor Palmeira.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Alfacinha Source Code

:: MORE INFORMATION

 

 

EvolSimulator 2.1.0 – Simulation Test Bed for Hypotheses of Genome Evolution

EvolSimulator 2.1.0

:: DESCRIPTION

EvolSimulator is a program that allows the simulation of evolution at the level of genes, gene families, and whole genomes. It was designed with the goal of investigating evolutionary phenomena like biased mutation regimes in different lineages, complicated patterns of selective pressure across sequences, and the confounding effects of paralogy and lateral genetic transfer.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 EvolSimulator

:: MORE INFORMATION

Citation

Beiko, R.G. and Charlebois, R.L. (2007).
A simulation test bed for hypotheses of genome evolution.
Bioinformatics 23:825-831.

PCAViz 1.2 – Visualizing Molecular Dynamics Simulations in the Web Browser

PCAViz 1.2

:: DESCRIPTION

PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Python

:: DOWNLOAD

PCAViz

:: MORE INFORMATION

Citation

J Chem Inf Model, 59 (10), 4087-4092 2019 Oct 28
PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser
Sayuri Pacheco, Jesse C Kaminsky, Iurii K Kochnev, Jacob D Durrant

GEvolutionS – Genome Evolution Simulation

GEvolutionS

:: DESCRIPTION

GEvolutionS simulates an evolutionary Genome rearrangement scenario with different genome rearrange operations. It operates on the most general model of genomes with a mixed collection on linear and circular genomes. The simulation process includes all classical rearrangement operations such as dcj, fissions, fusions, inversions, translocations, transpositions with choosable quantum.

::DEVELOPER

N/A

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

GEvolutionS

:: MORE INFORMATION

N/A

 

RuleBender 2.3 – Biological Rule-based Modeling, Simulation, and Visualization

RuleBender 2.3

:: DESCRIPTION

RuleBender is a novel visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry.

::DEVELOPER

RuleBender team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 RuleBender

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012;13 Suppl 8:S3. doi: 10.1186/1471-2105-13-S8-S3. Epub 2012 May 18.
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry.
Smith AM1, Xu W, Sun Y, Faeder JR, Marai GE.