scrm 1.7.2 – Coalescent Simulator for Biological Sequences

scrm 1.7.2

:: DESCRIPTION

scrm (sequential coalescent with recombination model ) is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage.

::DEVELOPER

scrm team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 scrm

:: MORE INFORMATION

Citation

scrm: efficiently simulating long sequences using the approximated coalescent with recombination.
Staab PR, Zhu S, Metzler D, Lunter G.
Bioinformatics. 2015 Jan 8. pii: btu861

VarEff 1.2 – Detecting the Evolution of the Coalescent Effective Population Size

VarEff 1.2

:: DESCRIPTION

VarEff estimates the effective sizes from actual to ancestral time with a coalescent approach. It works on steps of constant size to resolve the probabilities by an approximation of maximum likelihood from a Bayesian posterior distribution.

::DEVELOPER

VarEff Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R pacakge

:: DOWNLOAD

 VarEff

:: MORE INFORMATION

Citation

Chevalet C & Nikolic N. 2010.
Distribution of coalescent times and distances between microsatellite alleles with changing effective population size.
Theoretical Population Biology. Volume 77, Issue 3: 152-163

Modeler4Simcoal2 – Demography and Chromosome Modeler for Coalescent Simulations

Modeler4Simcoal2

:: DESCRIPTION

modeler4simcoal2 (m4s2) is a modeler for coalescent processes. It allows the modeling of both demographies and chromosomes (i.e., markers with linkage relationships in multiple chromosome blocks).

::DEVELOPER

Modeler4Simcoal2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows wity Cygwin /MacOsX
  • Java
:: DOWNLOAD

 Modeler4Simcoal2

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jul 15;23(14):1848-50. Epub 2007 May 8.
MODELER4SIMCOAL2: a user-friendly, extensible modeler of demography and linked loci for coalescent simulations.
Antao T1, Beja-Pereira A, Luikart G.

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

Associate Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 Microsat

:: MORE INFORMATION

MSMS 3.2rcb122 / MSMSPlay – Coalescent Simlation tool with Selection / Exploration of Basic Population Genetic Theory

MSMS 1.3 / MSMSPlay

:: DESCRIPTION

MSMS is a coalescent simulator that models itself off Hudsons ms in usage and includes selection. It is fast, often faster than ms, and portable running on Mac OSX, windows and Linux. By using this tool, one can study the patterns of selection in complicated demographic scenarios.

MSMSPlay is a GUI designed for simple exploration of basic population genetic theory. Its meant for exploratory runs with some useful output in an interactive fashion.

::DEVELOPER

The Mathematics and BioSciences Group

:: SCREENSHOTS

MSMSPlay

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 MSMS / MSMSPlay

:: MORE INFORMATION

Citation

Ewing G. and Hermisson J. (2010).
MSMS: A coalescent simulation program including recombination, demographic structure, and selection at a single locus.
Bioinformatics 26: 2064-2065.

CAMP – Coalescent based Association Mapping

CAMP

:: DESCRIPTION

CAMP (Coalescent based Association MaPping) is a tool for association studies.It takes into account the trade-off between the complexity of the genealogy and the power lost due to the additional multiple hypotheses.

::DEVELOPER

Gad Kimmel

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CAMP

:: MORE INFORMATION

Citation

Gad Kimmel et al.
Association Mapping and Significance Estimation via the Coalescent
Am J Hum Genet. 2008 December 12; 83(6): 675–683.

GeneRecon 1.2.1 – Coalescent based Tool for Fine-scale Association Mapping

GeneRecon 1.2.1

:: DESCRIPTION

GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position.

::DEVELOPER

Thomas Mailund

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GeneRecon

:: MORE INFORMATION

Citation:

Mailund T, Schierup MH, Pedersen CN, Madsen JN, Hein J, Schauser L.
GeneRecon–a coalescent based tool for fine-scale association mapping.
Bioinformatics. 2006 Sep 15;22(18):2317-8.

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.

GENOME 0.2 – Rapid Coalescent-based Whole Genome Simulator

GENOME 0.2

:: DESCRIPTION

GENOME is a program to simulate sequences drawn from a population under the Wright-Fisher neutral model (Ewens 1979). The purpose of this program is to simulate sequences on the whole genome scale within practical time. The program can be used to study the sampling properties of any statistics from a genome-wide study or to evaluate the performance of any method that is applied to genome-wide scale data.

::DEVELOPER

Liming Liang, @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / SunOS

:: DOWNLOAD

 GENOME

:: MORE INFORMATION

Citation

Liang L., Zollner S., Abecasis G.R. (2006)
GENOME: a rapid coalescent-based whole genome simulator