MFDM protocols

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MFDM specifications

Information


Unique identifier OMICS_25112
Name MFDM
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Hai-Peng Li <>

Additional information


http://www.picb.ac.cn/evolgen/softwares/download/MFDM_readMe_1.1.txt

Publication for MFDM

MFDM in pipeline

2014
PMCID: 4172856
PMID: 25216916
DOI: 10.1186/s12862-014-0198-8

[…] fs values at each locus. since deviations found using these tests could be caused by selection and/or demographic processes (e.g. population expansion and/or bottlenecks), we also performed the li’s mfdm test [], which is more robust in the presence of population size changes. finally, genetree [,] was used to infer the estimated age of selected variants and the time of the most recent common […]


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MFDM in publications

 (6)
PMCID: 5385031
PMID: 28405579
DOI: 10.1186/s40709-017-0064-0

[…] to the difference in snp density between regions in genomes., in 2011, li et al. [] presented a neutrality test that detects selective sweep regions using the maximum frequency of derived mutations (mfdm), which is a paramount signature of a selective sweep. according to [], the mfdm test is robust to processes that occur in a single and isolated population. […]

PMCID: 4432373
PMID: 25977142
DOI: 10.1038/srep10216

[…] from neutrality at individual locus. all six species were tested in turn with j. communis as the outgroup, and we found no significant deviation from the neutral model (). additionally, the mfdm test indicated that there was a significant probability (p = 0.0174) of selection at the cc1333 locus in j. microsperma. additionally, at cc1333 (p = 0.057) and pgi (p = 0.057) in j. […]

PMCID: 4416911
PMID: 25933225
DOI: 10.1371/journal.pone.0125199

[…] index r2 [] for each pair of variable sites, and its associated probability calculated by permutations., departures from the neutral equilibrium model were tested by the tajima′s dt test [] and the mfdm test [], which has the advantage of being free from the confounding signatures of demography., the program dnasp was also used to count the number of intraspecific polymorphisms, as well […]

PMCID: 4381672
PMID: 25834723
DOI: 10.1186/s13323-015-0023-1

[…] the fu and li’s d statistic [] takes advantage of low-frequency variation that is enriched in regions that recently underwent genetic hitchhiking. the maximum frequency of derived mutations (mfdm) test [] utilizes the mfdm to estimate the presence of an unbalanced tree topology in a given sample that is thought to arise in the adjacency of a locus that is under positive selection due […]

PMCID: 4172856
PMID: 25216916
DOI: 10.1186/s12862-014-0198-8

[…] fs values at each locus. since deviations found using these tests could be caused by selection and/or demographic processes (e.g. population expansion and/or bottlenecks), we also performed the li’s mfdm test [], which is more robust in the presence of population size changes. finally, genetree [,] was used to infer the estimated age of selected variants and the time of the most recent common […]


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MFDM institution(s)
Laboratory of Evolutionary Genomics, Department of Computational Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
MFDM funding source(s)
Supported by DFG-SFB680, the Shanghai Pujiang Program (08PJ14104), and the Bairen Program.

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