GSR: Simulator - MaCS

Basic Package Attributes
AttributeValue
Title MaCS
Short Description Markovian Coalescent Simulator
Long Description MaCS is a simulator of the coalescent process that simulates geneologies spatially across chromosomes as a Markovian process. The algorithm is similar to the SMC algorithm (McVean and Cardin, Phil Trans Soc R B 2005) in that the algorithm scales linearly in time with respect to sample size and sequence length. However, it more accurately models the true coalescent, while supporting all demographic scenarios found in the popular program MS (Hudson, Bioinformatics 2002) making this program appropriate for simulating data for structured populations in genome wide association studies.
Version 0.4f
Project Started 2011
Last Release 8 years, 2 months ago
Homepagehttps://github.com/gchen98/macs
Citations Chen GK, Marjoram P, Wall JD, Fast and flexible simulation of DNA sequence data., Genome Res, 01-01-2009 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated10-17-2019 (365 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsBiallelic Marker,
Simulation MethodStandard Coalescent,
Input
Data Type
File formatMS,
Output
Data TypeGenotype or Sequence, Phenotypic Trait, Mutation,
Sequencing Reads
File FormatMS,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline,
Gene FlowIsland Models,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationVarying Recombination Rates,
Mutation Models
Events AllowedVarying Demographic Features, Other,
Other
InterfaceCommand-line,
Development
Tested PlatformsLinux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application, Support,

The following 6 publications are selected examples of applications that used MaCS.

2018

Schumer M, Xu C, Powell DL, Durvasula A, Skov L, Holland C, Blazier JC, Sankararaman S, Andolfatto P, Rosenthal GG, et al., Natural selection interacts with recombination to shape the evolution of hybrid genomes., Science, 05-11-2018 [Abstract]

2017

Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, et al., Loci associated with skin pigmentation identified in African populations., Science, 11-17-2017 [Abstract]

2016

Browning BL, Browning SR, Genotype Imputation with Millions of Reference Samples., Am J Hum Genet, 01-07-2016 [Abstract]

Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF, Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies., Genome Res, 03-01-2016 [Abstract]

Vernot B, Tucci S, Kelso J, Schraiber JG, Wolf AB, Gittelman RM, Dannemann M, Grote S, McCoy RC, Norton H, et al., Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals., Science, 04-08-2016 [Abstract]

Kelleher J, Etheridge AM, McVean G, Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes., PLoS Comput Biol, 05-04-2016 [Abstract]


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