Tag: Simulate

quantiNEMO 1.0.4 – Simulate Quantitative Traits with Explicit Genetic Architecture

quantiNEMO 1.0.4

:: DESCRIPTION

quantiNEMO is an individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population. quantiNEMO was developed to investigate the effects of selection, mutation, recombination, and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a heterogeneous habitat. quantiNEMO is highly flexible at various levels: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, mating system, etc.

::DEVELOPER

Samuel Neuenschwander, Jérôme Goudet, Frédéric Hospital, andFrédéric Guillaume.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

quantiNEMO

:: MORE INFORMATION

Citation

Neuenschwander S, Hospital F, Guillaume F, Goudet J (2008)
quantiNEMO: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation
Bioinformatics 24, 1552-1553.

SIMULATOR 1.0 – Simulate DNA and Protein datasets with well-defined Insertion-deletion dynamics

SIMULATOR 1.0

:: DESCRIPTION

SIMULATOR is a software to simulate DNA and protein datasets with well-defined insertion-deletion dynamics according to a user-given tree.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SIMULATOR

:: MORE INFORMATION

Citation:

Roland Fleißner (2004) Sequence alignment and phylogenetic inference. Logos Verlag, Berlin.

HGT – Simulate and Estimate Horizontal Gene Transfer events

HGT

:: DESCRIPTION

HGT is a software to simulate and estimate Horizontal Gene Transfer events.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HGT

:: MORE INFORMATION

Citation:

Simone Linz, Achim Radtke, Arndt von Haeseler
A Likelihood Framework to Measure Horizontal Gene Transfer
Molecular Biology and Evolution, 24:1312-1319, 2007.

TWINSIM – Simulate Twin-nuclear Families in which QTLs and Linked Markers are Segregating

TWINSIM

:: DESCRIPTION

TWINSIM generates nuclear families, a proportion of which contain monozygotic twins, in which multiple quantitative trait loci are segregating. One of these QTLs is linked to multiple markers. Families can be selected to contain high and/or low values at the quantitative or ordinal trait.

::DEVELOPER

David Duffy

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /MacOsX /  Linux
  • Frotran 77

:: DOWNLOAD

 TWINSIM

:: MORE INFORMATION

GenoQuickSim 20100309 – Simulates Genotypic data using Coalescent Methods

GenoQuickSim 20100309

:: DESCRIPTION

GenoQuickSim is a software for conveniently simulating genotypic data for simple poulation structures

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 GenoQuickSim

:: MORE INFORMATION

ChromoSeg 1.0 – Simulate and plot Ancestral Recombination Graphs

ChromoSeg 1.0

:: DESCRIPTION

ChromoSeg. A simulation program that simulates and plots (in real time) ancestral recombination graphs

::DEVELOPER

Eric C. Anderson

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 ChromoSeg

:: MORE INFORMATION

SelSim 2.1 – Simulate Population Genetic Data with Selection and Recombination

SelSim 2.1

:: DESCRIPTION

SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recombining region within which a single bi-allelic site has experienced natural selection. SelSim allows simulation from either a fully stochastic model of, or deterministic approximations to, natural selection within a coalescent framework. A number of different mutation models are available for simulating surrounding neutral variation. The package enables a detailed exploration of the effects of different models and strengths of selection on patterns of diversity.

::DEVELOPER

Chris C A Spencer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/WIndows

:: DOWNLOAD

 SelSim

:: MORE INFORMATION

Citation

Spencer C., Coop, G. (2005)
SelSim: A program to simulate population genetic data with selection and recombination.
Bioinformatics. 2004 Dec 12;20(18):3673-5.

CoaCC 1.0.1 – Simulate Case-control Study using Coalescent Framework

CoaCC 1.0.1

:: DESCRIPTION

CoaCC simulates a case-control study using a coalescent framework. It assumes a haploid sample of cases and a second haploid sample of controls. Of these two samples the genealogy is generated, dependent on the user-specified population history. From this genealogy a distribution of marker-haplotypes is generated by allowing for marker-mutation and recombinations between marker and gene as well as between markers.

::DEVELOPER

Sebastian Zöllner @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Complier

:: DOWNLOAD

 CoaCC

:: MORE INFORMATION

If you use CoaCC please e-mail szoellne@umich.edu or fill out the registration form.

Phylogen 1.1 – Simulate Phylogenies

Phylogen 1.1

:: DESCRIPTION

Phylogen implements some straight-forward birth-death models for simulating phylogenies. It is intended to be fast and flexible and can simulate very large trees (depending on memory and speed of computer). It will then optionally reconstruct trees only containing extant lineages or produce trees containing a random sample of lineages. Trees can be written to a file for analysis in other packages. It will also draw lineages-through-time-plots.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Phylogen

:: MORE INFORMATION