MetaPASSAGE – Automated Simulations and Analysis of Gene Families

MetaPASSAGE

:: DESCRIPTION

MetaPASSAGE, a software pipeline to generate in silico bacterial communities, simulates a sample of shotgun reads from a gene family represented in the community, orient or translate reads, and produce a profile-based alignment of the reads from which a gene-family phylogenetic tree can be built.

::DEVELOPER

Pollard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 MetaPASSAGE

:: MORE INFORMATION

Citation

BMC Genomics. 2013 Jun 22;14:419. doi: 10.1186/1471-2164-14-419.
Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.
Riesenfeld SJ, Pollard KS.

SIMCOAL 2.1.2 – Simulation of Molecular data in interconnected Populations with Arbitrary Demography

SIMCOAL 2.1.2

:: DESCRIPTION

SIMCOAL (SIMulate COAlescence) is a computer program for the simulation of molecular genetic diversity in an arbitrary number of haploid populations examined for a set of fully linked loci.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 SIMCOAL

:: MORE INFORMATION

Citation

Excoffier, Novembre, Schneider (2000),
SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography“,
Journal of Heredity, 91:506-509.

AEGIS – Augmented Exploration of the GO with Interactive Simulations

AEGIS

:: DESCRIPTION

AEGIS is an open-source software with an interactive information-retrieval framework that enables an investigator to navigate through the entire Gene Ontology (GO) graph (with tens of thousands of nodes) and focus on fine-grained details without losing the context.

::DEVELOPER

the Sabatti Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX / Linux
  • Python

:: DOWNLOAD

AEGIS

:: MORE INFORMATION

Citation

Zhu J, Zhao Q, Katsevich E, Sabatti C.
Exploratory Gene Ontology Analysis with Interactive Visualization.
Sci Rep. 2019 May 24;9(1):7793. doi: 10.1038/s41598-019-42178-x. PMID: 31127124; PMCID: PMC6534545.

AlphaSimR 0.13.0 – Breeding Program Simulations

AlphaSimR 0.13.0

:: DESCRIPTION

AlphaSimR is the successor to the AlphaSim software for breeding program simulation and a package for the R software environment. AlphaSimR builds on lessons learned from development of our previous software and the use of this software to perform simulations of breeding programs. The result is a software package this is both easy-to-use and flexible. This ease-of-use and flexibility provides users with the ability to simulate a wide range of complex plant and animal breeding programs.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R

:: DOWNLOAD

AlphaSimR

:: MORE INFORMATION

Citation

Gaynor RC, Gorjanc G, Hickey JM.
AlphaSimR: an R package for breeding program simulations.
G3 (Bethesda). 2021 Feb 9;11(2):jkaa017. doi: 10.1093/g3journal/jkaa017. PMID: 33704430; PMCID: PMC8022926.

AlphaMPSim R1 – Flexible Simulation of Multi-parent Crosses

AlphaMPSim R1

:: DESCRIPTION

AlphaMPSim is s simple software package for simulating data in multi-parent populations.

::DEVELOPER

John Hickey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • R package

:: DOWNLOAD

 AlphaMPSim

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 28. pii: btu206. [Epub ahead of print]
AlphaMPSim: flexible simulation of multi-parent crosses.
Hickey JM1, Gorjanc G2, Huang BE2.

Biocellion 1.2 – Computer Simulation of Living Cell Systems

Biocellion 1.2

:: DESCRIPTION

Biocellion is an agent-PDE (Partial Differential Equation) based simulation framework, designed for solving general models of multicellular biological systems.

::DEVELOPER

Shmulevich Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

 Biocellion

:: MORE INFORMATION

Citation

Biocellion: accelerating computer simulation of multicellular biological system models.
Kang S, Kahan S, McDermott J, Flann N, Shmulevich I.
Bioinformatics. 2014 Jul 26. pii: btu498.

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.