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MSMS specifications


Unique identifier OMICS_04381
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


No version available


Publication for MSMS

MSMS citations


Human local adaptation of the TRPM8 cold receptor along a latitudinal cline

PLoS Genet
PMCID: 5933706
PMID: 29723195
DOI: 10.1371/journal.pgen.1007298

[…] appeared as in the SDN model (tmut~U(30,000, 60,000 years ago)) but was completely neutral.We ran one million simulations for each selection model and 100,000 simulations for the neutral model using msms []. Each simulation comprised a stretch of 185 kb with 122 chromosomes of an African (population 1) and a non-African (population 2) population. Human demographic parameters followed the model in […]


Hybridization and gene flow in the mega pest lineage of moth, Helicoverpa

Proc Natl Acad Sci U S A
PMCID: 5948968
PMID: 29610329
DOI: 10.1073/pnas.1718831115

[…] s 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 for H […]


Signatures of Long Term Balancing Selection in Human Genomes

Genome Biol Evol
PMCID: 5952967
PMID: 29608730
DOI: 10.1093/gbe/evy054

[…] NCD’s power was evaluated by simulations (under neutrality and with selection) with MSMS () following the demographic model described in for African, European, and East Asian human populations, and considering a generation time of 25 years, mutation rate of 2.5×10−8 per site, recomb […]


Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex

Proc Natl Acad Sci U S A
PMCID: 5777044
PMID: 29279400
DOI: 10.1073/pnas.1713288114

[…] s (, , ), genetic divergence along the genome was highly heterogeneous, irrespective of the level of genome-wide differentiation and geographical separation. In addition, coalescent simulations using msms () under the best-fitting demographic model showed that the distributions of simulated polymorphisms and divergence were generally in agreement with the observed patterns across the genome (). Th […]


A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants

Genome Biol Evol
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 rat […]


Powerful Inference with the D Statistic on Low Coverage Whole Genome Data

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

[…] 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 of the s […]


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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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