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GSR: Simulator - MaCS
| Attribute | Value |
|---|---|
| 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 | 11 years, 8 months ago |
| Homepage | https://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 Certification |  ✔ Accessibility |
| Last evaluated | 10-17-2019 (1640 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, |
| Variations | Biallelic Marker, |
| Simulation Method | Standard Coalescent, |
| Input | |
| Data Type | |
| File format | MS, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, Mutation, |
| Sequencing Reads | |
| File Format | MS, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, |
| Gene Flow | Island Models, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Varying Recombination Rates, |
| Mutation Models | |
| Events Allowed | Varying Demographic Features, Other, |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Linux and Unix, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 6
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]