SIMULATE – Simulate Genotypes in Family Members

SIMULATE

:: DESCRIPTION

SIMULATE is a program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package.

(1) SIMULATE is essentially the original version, in which all marker genotypes are generated based on population marker characteristics (allele frequencies, etc.) and recombination fractions between them.

(2) SIMULATE2 assumes that for founder individuals with known genotypes (i.e., they are “typed”) the original (observed) genotypes are provided. These genotypes will not be modified (generated) in the course of the simulations. For founders with unknown genotypes (“untyped”), marker genotypes will be generated as in the SIMULATE program. However, prior to running SIMULATE2, users may want to impute such genotypes from the original data so that few founders have unknown genotypes. The two program versions have somewhat different input requirements. For example, the random number generator is different –SIMULATE requires 3 seeds and SIMULATE2 requires only one.

(3) SIMULATE3 is an extension of SIMULATE in that markers must be SNPs (have only two alleles) and may be correlated (in linkage disequilibrium) with each other (see below how these correlations are generated). Also, this program version incorporates an updated random number generator, ran (int64) .

::DEVELOPER

Joe Terwilliger &  Jurg Ott, Ph.D.

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 simulate

Citation

Terwilliger JD, Speer M, Ott J:
Chromosome-based method for rapid computer simulation in human genetic linkage analysis.
Genet Epidemiol 1993;10:217-224.

HAPGEN 2.2.0 – Simulate Case Control Datasets at SNP Markers

HAPGEN 2.2.0

:: DESCRIPTION

HAPGEN simulates case control datasets at SNP markers. The new version can now simulate multiple disease SNPs on a single chromosome, on the assumption that each disease SNP acts independently and are in Hardy-Weinberg equilibrium. We also supply a R package that can simulate interaction between the disease SNPs.

::DEVELOPER

Jonathan Marchini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX /  Linux

:: DOWNLOAD

 HAPGEN

:: MORE INFORMATION

Citation

Chris C. A. Spencer, Zhan Su, Peter Donnelly, Jonathan Marchini (2009)
Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip.
PLoS Genet 5(5).

AQUASPLATCHE 1.1 – Simulate Genetic Diversity based on a Realistic Vectorized Environment

AQUASPLATCHE 1.1

:: DESCRIPTION

AQUASPLATCHE starts by dividing a realistic vectorized network of river streams into segments of arbitrary length. The program then proceeds by simulating the colonization of the streams from an arbitrary source, recording the evolution of the segment densities and the migration events between adjacent segments over time. This demographic history is then used to generate genetic data of population samples located in various segments of the river system, using a backward coalescent framework.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 AQUASPLATCHE

:: MORE INFORMATION

Citation

Neuenschwander S (2006)
AQUASPLATCHE: a program to simulate genetic diversity in populations living in linear habitats.
Molecular Ecology Notes 6 583-585.

PSPE – Simulate Evolution of Non-coding DNA Sequences

PSPE

:: DESCRIPTION

PSPE (Phylogenetic Simulation of Promoter Evolution) is a computational tool specifically designed for simulating evolution of non-coding DNA sequences, in particular promoter sequences.

::DEVELOPER

PSPE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PSPE

:: MORE INFORMATION

Citation

Weichun Huang, Joseph R Nevins, and Uwe Ohler,
Phylogenetic simulation of promoter evolution: estimation and modelling of binding site turnover events and assessing their impact on alignment tools,
Genome Biology, Vol 8 (10) 2007

Microsat – Simulates the Evolution of Linked and unlinked Microsatellites using the Coalescent

Microsat

:: DESCRIPTION

Microsat reads coalescent genealogies generated by Richard Hudson’s ms, and translates them into short tandem repeat (STR, or microsatellite) datasets using the single step mutation model (SMM).

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 Microsat

:: MORE INFORMATION

bnpsd 1.2.3 – Model and Simulate Admixed Populations

bnpsd 1.2.3

:: DESCRIPTION

bnpsd (Balding-Nichols Pritchard-Stephens-Donnelly) is an R package to model and simulate admixed populations

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

bnpsd

:: MORE INFORMATION

Citation

Ochoa, Alejandro, and John D. Storey. 2016a.
FST And Kinship for Arbitrary Population Structures I: Generalized Definitions.”
bioRxiv doi:10.1101/083915.

Ochoa, Alejandro, and John D. Storey. 2016b.
FST And Kinship for Arbitrary Population Structures II: Method of Moments Estimators.
bioRxiv doi:10.1101/083923.

Pyvolve v1.0.1 – Python Library to Simulate Evolutionary Sequence data

Pyvolve v1.0.1

:: DESCRIPTION

Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution.

::DEVELOPER

Claus Wilke’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pyvolve

:: MORE INFORMATION

Citation

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.
Spielman SJ, Wilke CO.
PLoS One. 2015 Sep 23;10(9):e0139047. doi: 10.1371/journal.pone.0139047.

simNGS 20130502 – Simulate Observations from Illumina NGS machines

simNGS 20130502

:: DESCRIPTION

simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be present in real data (“dust”, bubbles, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 simNGS

:: MORE INFORMATION

SimulaTE 1.13 – Simulating Complex Landscapes of Transposable Elements of Populations

SimulaTE 1.13

:: DESCRIPTION

SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.

::DEVELOPER

Institute of Population Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

SimulaTE

:: MORE INFORMATION

Citation:

SimulaTE: simulating complex landscapes of transposable elements of populations.
Kofler R.
Bioinformatics. 2018 Apr 15;34(8):1419-1420. doi: 10.1093/bioinformatics/btx772.

Seq-Gen 1.3.4 – Simulate the Evolution of Sequences along a Phylogeny

Seq-Gen 1.3.4

:: DESCRIPTION

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Seq-Gen

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Jun;13(3):235-8.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
Rambaut A1, Grassly NC.