GSR: Simulator - mbs

Basic Package Attributes
AttributeValue
Title mbs
Short Description modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection
Long Description A software application to generate samples of DNA sequences when there is a biallelic site targeted by selection. mbs is developed by modifying Hudson's ms. The mbs software is so flexible that it can incorporate any arbitrary histories of population size changes and any mode of selection as long as selection is operating on a biallelic site.
Project Started 2008
Last Release 11 years, 10 months ago
Homepagehttp://www.sendou.soken.ac.jp/esb/innan/InnanLab/software.html
Citations Teshima KM, Innan H, mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection., BMC Bioinformatics, 05-30-2009 [ Abstract, cited in PMC ]
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Last evaluated02-06-2020 (253 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
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsBiallelic Marker,
Simulation MethodStandard Coalescent,
Input
Data Type
File formatMS,
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatMS,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesExponential Growth or Decline,
Gene FlowIsland Models,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
ModelsDirectional Selection, Balancing Selection,
RecombinationVarying Recombination Rates,
Mutation Models
Events AllowedVarying Demographic Features,
Other
InterfaceCommand-line,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++,
License
GSR CertificationDocumentation,

The following 8 publications are selected examples of applications that used mbs.

2019

Kim KW, Jackson BC, Zhang H, Toews DPL, Taylor SA, Greig EI, Lovette IJ, Liu MM, Davison A, Griffith SC, et al., Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird., Nat Commun, 04-23-2019 [Abstract]

2018

Alachiotis N, Pavlidis P, RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectors., Commun Biol, 06-27-2018 [Abstract]

Mathieson S, Mathieson I, FADS1 and the Timing of Human Adaptation to Agriculture., Mol Biol Evol, 12-01-2018 [Abstract]

2014

Ferrer-Admetlla A, Liang M, Korneliussen T, Nielsen R, On detecting incomplete soft or hard selective sweeps using haplotype structure., Mol Biol Evol, 05-01-2014 [Abstract]

Huerta-Sánchez E, Jin X, Asan, Bianba Z, Peter BM, Vinckenbosch N, Liang Y, Yi X, He M, Somel M, et al., Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA., Nature, 08-14-2014 [Abstract]

2013

Wills DM, Whipple CJ, Takuno S, Kursel LE, Shannon LM, Ross-Ibarra J, Doebley JF, From many, one: genetic control of prolificacy during maize domestication., PLoS Genet, 06-01-2013 [Abstract]

Zhao L, Lascoux M, Overall AD, Waxman D, The characteristic trajectory of a fixing allele: a consequence of fictitious selection that arises from conditioning., Genetics, 11-01-2013 [Abstract]

2012

Chan AH, Jenkins PA, Song YS, Genome-wide fine-scale recombination rate variation in Drosophila melanogaster., PLoS Genet, 01-01-2012 [Abstract]


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