PhyloSim 3.0.5 – Monte Carlo Simulation of Sequence Evolution

PhyloSim 3.0.5

:: DESCRIPTION

PhyloSim is an extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhyloSim

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Apr 19;12:104.
PhyloSim – Monte Carlo simulation of sequence evolution in the R statistical computing environment.
Sipos B, Massingham T, Jordan GE, Goldman N.

IBDSim 2.0 – Simulation of Genotypic data under general Isolation by Distance models

IBDSim 2.0

:: DESCRIPTION

IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models.

::DEVELOPER

Raphael Leblois

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 IBDSim

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2009 Jan;9(1):107-9. doi: 10.1111/j.1755-0998.2008.02417.x. Epub 2008 Nov 10.
IBDSim: a computer program to simulate genotypic data under isolation by distance.
Leblois R, Estoup A, Rousset F.

SLiM 3.3.1 – Forward Population Genetic Simulation

SLiM 3.3.1

:: DESCRIPTION

SLiM (Selection on Linked Mutations) is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated evolutionary scenarios.

::DEVELOPER

Messer Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX
:: DOWNLOAD

SLiM

:: MORE INFORMATION

Citation

SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model.
Haller BC, Messer PW.
Mol Biol Evol. 2019 Mar 1;36(3):632-637. doi: 10.1093/molbev/msy228.

SDSE 2.0 – Simulation of DNA Sequence Evolution

SDSE 2.0

:: DESCRIPTION

SDSE is an  algorithm  to  simulate  DNA  sequence  evolution  under  a  general  stochastic  model,  including  as  particular  cases  all  the  previously  used  schemes  of  nucleotide  substitution

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

SDSE

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

 SDSE

:: MORE INFORMATION

Citation:

Comput Appl Biosci. 1989 Feb;5(1):47-50.
SDSE: a software package to simulate the evolution of a pair of DNA sequences.
Oliver JL, Marín A, Medina JR.

GetCrosses 0.5b – Simulation of Offspring Genotypes from a SNPs file

GetCrosses 0.5b

:: DESCRIPTION

GetCrosses is a computer program written in Perl scripting language that simulates offspring genotypes from a SNPs file for their use in relatedness analysis. Simulations are performed along given pedigrees. Following these pedigrees, individuals are computationally crossed by randomly selecting one allele of each locus from each parent to generate the alleles of a new individual. The new individuals generated in this manner are added to the output file and can be crossed with other individuals of the pedigree.

::DEVELOPER

Castresana Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOs
  • Perl

:: DOWNLOAD

GetCrosses

:: MORE INFORMATION

Citation:

Escoda, L., González-Esteban, J., Gómez, A., and Castresana, J. (2017).
Using relatedness networks to infer contemporary dispersal: application to the endangered mammal Galemys pyrenaicus.
Molecular Ecology 26, 3343-3357.

MySSP 1.0.3.5 – Simulation of DNA Sequence Evolution across a Phylogenetic Tree

MySSP 1.0.3.5

:: DESCRIPTION

MySSP is a program for the simulation of DNA sequence evolution across a phylogenetic tree

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

MySSP

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MySSP

:: MORE INFORMATION

Citation

Rosenberg, M.S. (2005)
MySSP: Non-stationary evolutionary sequence simulation, including indels.
Evolutionary Bioinformatics Online 1:81–83

MemGen – Setting up Membrane Simulation systems

MemGen

:: DESCRIPTION

MemGen (Membrane Generator) creates multi-component lipid bilayer membranes for molecular dynamics simulations.

::DEVELOPER

Computational Biophysics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2015 May 7. pii: btv292.
MemGen: A general web server for the setup of lipid membrane simulation systems.
Knight CJ, Hub JS

SCNVSim 1.3.1 – Simulation of Somatic CNV and Strucuture Variants

SCNVSim 1.3.1

:: DESCRIPTION

SCNVSim is a Bioinformaitcs tool developed in Java programming language for the simulation of somatic copy number variations and structure variations in cancer genome studies.

::DEVELOPER

SCNVSim team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 SCNVSim

:: MORE INFORMATION

Citation

SCNVSim: somatic copy number variation and structure variation simulator.
Qin M, Liu B, Conroy JM, Morrison CD, Hu Q, Cheng Y, Murakami M, Odunsi AO, Johnson CS, Wei L, Liu S, Wang J.
BMC Bioinformatics. 2015 Feb 28;16(1):66.

Rosetta 3.11 – Simulation and Design of Protein

Rosetta 3.11

:: DESCRIPTION

ROSETTA is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

::DEVELOPER

Rosetta Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Rosetta

:: MORE INFORMATION

Citation

Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popovi? Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P (2011)
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
Methods Enzymol 487:545-74

CS-PSeq-Gen 1.0 – Simulation of Protein Sequences under Constraints

CS-PSeq-Gen 1.0

:: DESCRIPTION

CS-PSeq-Gen is a program derived from PSeq-Gen, a program developed by Nick C. Grassly and Andrew Rambaut, designed to simulate the evolution of protein sequences along evolutionary trees. CS-PSeq-Gen modifications are related to the aim of simulating the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny: the “root sequence” that initiates the simulation, or the rate heterogeneity among sites are specific on each particular protein family. CS-Pseq-Gen will allow simulations to take such information into account. As well, exploring the evolution of one protein family and testing hypotheses makes often it necessary to have some control on the variability of the parameters. CS-PSeq-Gen will allow some control on the simulated tree / branch lengths around an average value. Finally, a particular category of applications for such simulations is the search for the significant co-evolution of sites. CS-PSeq-Gen offers some facilities to generate sequences under such hypotheses, and propose a basic scheme for their detection, that can be easily adapted by programmers.

::DEVELOPER

P. Tufféry  (tuffery@ebgm.jussieu.fr )

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CS-PSeq-Gen

:: MORE INFORMATION

Citation

Tufféry, P.
CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints
Bioinformatics, Volume 18, Number 7, July 2002 , pp. 1015-1016(2)