MSMS protocols

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MSMS specifications

Information


Unique identifier OMICS_04381
Name MSMS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for MSMS

MSMS in pipelines

 (2)
2017
PMCID: 5767965
PMID: 29228179
DOI: 10.1093/gbe/evx262

[…] in our population, namely the positive tajima’s d. for example, a population bottleneck would produce negative values of tajima’s d, and thus is not considered here. populations were simulated using msms () with a population size of 2×106 () for regions of 105 bp. we sampled 170 individuals to match the depth of our data and assumed a neutral mutation rate of μ = 3×10−9 () and a recombination […]

2016
PMCID: 4910016
PMID: 27292132
DOI: 10.1038/ncomms11855

[…] families (), we extracted clr estimates for each gene family based on the coordinates within the bed files (see above)., coalescent simulations to determine outlier fst values were carried out using msms., the topology of the model was based on the previously computed genome-wide fst, but with a forced polytomy between the short terminal branches of the netherlands, ithaca and tasmania […]


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MSMS in publications

 (19)
PMCID: 5948968
PMID: 29610329
DOI: 10.1073/pnas.1718831115

[…] calculated for both subspecies of h. armigera () using the inferred effective population size histories as detailed by the pairwise sequentially markovian coalescent (psmc) analyses as the basis of msms (v. 1.3) simulations (), opting for 100 simulated datasets over 1 mb. in addition, nonnegative, weighted fst was calculated across 10-kb windows (≥50 snps) in autosomes and the z chromosome […]

PMCID: 5767965
PMID: 29228179
DOI: 10.1093/gbe/evx262

[…] the range of mutations rates for sweeps was between 0 and 0.5, where anything 0.2 and below was primarily hard. the beneficial allele was always placed at the center of the locus. for all msms simulations, tajima’s d was output using the –otpi flag within the program, and h12 was calculated for each simulated population using scripts from ()., we wanted to investigate possible […]

PMCID: 5919751
PMID: 29196497
DOI: 10.1534/g3.117.300192

[…] for which e [dun] = 0. in this way, an estimate of the admixture rate was obtained for the topology of figure s3a in file s1., different scenarios have been generated using the coalescent simulator msms () to reproduce the trees of , in which times are in units of generations. each topology has been simulated 100 times for a constant population size of ne=104. mutation and recombination […]

PMCID: 5645465
PMID: 29042606
DOI: 10.1038/s41598-017-13901-3

[…] model of molecular evolution i also calculated tajima’s d in 10 kb windows using vcftools. to assess the significance of deviations in tajima’s d and π 10,000 simulations were performed using msms conditioned on the number of variable sites and with no recombination., linkage between wolbachia and mtdna snps could potentially be a predictor of co-inheritance of mtdna and wolbachia. […]

PMCID: 5574762
PMID: 28861239
DOI: 10.1002/ece3.3190

[…] early gene flow with 4 nm = 10, and unidirectional recent gene flow with 4 nm = 0.001, 0.01, 0.1, 1.0, and 10.0), we also investigated gene trees for regions adjacent to a selected locus using msms (ewing & hermisson, ), a coalescent simulator based on ms that incorporates forward‐in‐time simulations of selection on single loci. we modeled gene trees for 100 kb adjacent to a selected […]


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MSMS institution(s)
Department of Mathematics, University of Vienna, Vienna, Austria; Max F Perutz Laboratories, Vienna, Austria
MSMS funding source(s)
Deutsche Forschungsgemeinschaft (DFG); the Vienna Science and Technology Fund (WWTF)

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