mbs

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Basic Package Attributes
Attribute	Value
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, 6 months ago
Homepage	http://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, May 30, 2009 [Abstract, cited in PMC ]
GSR Certification	Accessibility ✔Documentation Application Support
Last evaluated	Feb. 6, 2020 (134 days ago)
Author verification	The 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 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,
Sequencing Reads
File Format	MS,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes	Exponential Growth or Decline,
Gene Flow	Island Models,
Spatiality
Life Cycle
Mating System	Random Mating,
Fecundity
Natural Selection
Determinant
Models	Directional Selection, Balancing Selection,
Recombination	Varying Recombination Rates,
Mutation Models
Events Allowed	Varying Demographic Features,
Other
Interface	Command-line,
Development
Tested Platforms	Mac OS X, Linux and Unix,
Language	C or C++,
License
GSR Certification	Documentation,

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

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, April 23, 2019 [Abstract]

Alachiotis N, Pavlidis P, RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectors., Commun Biol, June 27, 2018 [Abstract]
Mathieson S, Mathieson I, FADS1 and the Timing of Human Adaptation to Agriculture., Mol Biol Evol, Dec. 1, 2018 [Abstract]

Ferrer-Admetlla A, Liang M, Korneliussen T, Nielsen R, On detecting incomplete soft or hard selective sweeps using haplotype structure., Mol Biol Evol, May 1, 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, Aug. 14, 2014 [Abstract]

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, June 1, 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, Nov. 1, 2013 [Abstract]

Chan AH, Jenkins PA, Song YS, Genome-wide fine-scale recombination rate variation in Drosophila melanogaster., PLoS Genet, Jan. 1, 2012 [Abstract]