GSR: Simulator - msms

Basic Package Attributes
Title msms
Short Description A coalescent Simlation tool with selection.
Long Description This document describes how to use msms, a tool to generate sequence samples under both neutral models and a single locus selection model. msms permits the full range of demographic models provided by ms(Hudson, 2002). In partic-ular, it allows for multiple demes with arbitrary migration patterns, population growth and decay in each deme, and for population splits and mergers. Selection (including dominance) can depend on the deme and also change with time. The program is designed to be command line compatible to ms, however no prior knowledge of ms is assumed for this document. Applications of this program include power studies, analytical comparisons, approximated Bayesian computation among many others. Because most applications require the generation of a large number of independent replicates, the code is designed to be efficient and fast. For the neutral case, it is comparable to ms and even faster for large recombination rates. For selection, the performance is only slightly slower, making this one of the fastest tools for simulation with selection. The program has been developed with a wide number of possible operating systems and hardware in mind. For this reason, the code has been developed in Java and can run on any hardware that supports Java 1.6. This includes Mac OS X, all current versions of MS Windows, and most Unix flavors (Linux, Sun, BSD). The Java programing language is also popular and widely known which should facilitate the writing of extensions for the program.
Version 3.2rc-b75
Project Started 2010
Last Release 9 years, 11 months ago
Citations Ewing G, Hermisson J, MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus., Bioinformatics, 08-15-2010 [ Abstract, cited in PMC ]
GSR Certification


Last evaluated01-10-2019 (645 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Type of Simulated DataHaploid DNA Sequence,
VariationsBiallelic Marker,
Simulation MethodStandard Coalescent,
Data TypeAllele Frequencies,
File formatMS,
Data TypeGenotype or Sequence,
Sequencing ReadsOther,
File FormatMS,
Sample Type
Trait Type
Evolutionary Features
Population Size ChangesConstant Size, Exponential Growth or Decline,
Gene FlowIsland Models, User-defined Matrix,
Life Cycle
Mating SystemRandom Mating,
Natural Selection
RecombinationVarying Recombination Rates,
Mutation Models
Events AllowedVarying Demographic Features, Other,
InterfaceCommand-line, Script-based,
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application,

The following 7 publications are selected examples of applications that used msms.


Van Belleghem SM, Baquero M, Papa R, Salazar C, McMillan WO, Counterman BA, Jiggins CD, Martin SH, Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography., Mol Ecol, 10-01-2018 [Abstract]

Bitarello BD, de Filippo C, Teixeira JC, Schmidt JM, Kleinert P, Meyer D, Andrés AM, Signatures of Long-Term Balancing Selection in Human Genomes., Genome Biol Evol, 03-01-2018 [Abstract]

Key FM, Abdul-Aziz MA, Mundry R, Peter BM, Sekar A, D'Amato M, Dennis MY, Schmidt JM, Andrés AM, Human local adaptation of the TRPM8 cold receptor along a latitudinal cline., PLoS Genet, 05-03-2018 [Abstract]

Wang J, Ding J, Tan B, Robinson KM, Michelson IH, Johansson A, Nystedt B, Scofield DG, Nilsson O, Jansson S, et al., A major locus controls local adaptation and adaptive life history variation in a perennial plant., Genome Biol, 06-04-2018 [Abstract]

Hartasánchez DA, Brasó-Vives M, Heredia-Genestar JM, Pybus M, Navarro A, Effect of Collapsed Duplications on Diversity Estimates: What to Expect., Genome Biol Evol, 11-01-2018 [Abstract]

vonHoldt BM, Kartzinel RY, Huber CD, Le Underwood V, Zhen Y, Ruegg K, Lohmueller KE, Smith TB, Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus., Nat Commun, 11-19-2018 [Abstract]


Wetrich RM, Sidhu DS, Giant sigmoid diverticulum., West J Med, 06-01-1978 [Abstract]

Propose changes to this simulator