GSR: Simulator - mbs
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 | 15 years, 3 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, 05-30-2009 [ Abstract, cited in PMC ] |
GSR Certification | Accessibility |
Last evaluated | 02-06-2020 (1507 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. |
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, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 10
The following 10 publications are selected examples of applications that used mbs.
2023
Zhao H, Souilljee M, Pavlidis P, Alachiotis N, Genome-wide scans for selective sweeps using convolutional neural networks., Bioinformatics, 06-30-2023 [Abstract]
2021
Zeng K, Charlesworth B, Hobolth A, Studying models of balancing selection using phase-type theory., Genetics, 06-24-2021 [Abstract]
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]