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

scrm 1.7.4 – Coalescent Simulator for Biological Sequences

scrm 1.7.4

:: 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

G-PhoCS – Generalized Phylogenetic Coalescent Sampler

G-PhoCS

:: DESCRIPTION

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.

::DEVELOPER

Siepel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Python

:: DOWNLOAD

G-PhoCS

:: MORE INFORMATION

Citation

Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A.
Bayesian inference of ancient human demography from individual genome sequences.
Nat Genet. 2011 Sep 18;43(10):1031-4. doi: 10.1038/ng.937. PMID: 21926973; PMCID: PMC3245873.

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

:: 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

ASMC – Ascertained Sequentially Markovian Coalescent

ASMC

:: DESCRIPTION

The ASMC is a method to efficiently estimate pairwise coalescence times along the genome. It can be run using SNP array or whole-genome sequencing (WGS) data.

::DEVELOPER

Palamara Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
C++

:: DOWNLOAD

ASMC

:: MORE INFORMATION

Citation

Palamara PF, Terhorst J, Song YS, Price AL.
High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability.
Nat Genet. 2018 Sep;50(9):1311-1317. doi: 10.1038/s41588-018-0177-x. Epub 2018 Aug 13. PMID: 30104759; PMCID: PMC6145075.

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

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

:: 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.

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.