FREGENE protocols

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FREGENE specifications


Unique identifier OMICS_04167
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for FREGENE

FREGENE in pipeline

PMCID: 3337470
PMID: 22540033
DOI: 10.1534/g3.111.001297

[…] drop methods, was designed to be simple and flexible. it makes routine simulation of sequence data for large pedigrees possible. other genome simulation packages are publically available, such as fregene (), haplosim (), and qmsim (). however, given that these packages are based on gene dropping approaches they are less computationally efficient in comparison with the combination […]

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FREGENE in publications

PMCID: 5519584
PMID: 28785268
DOI: 10.3389/fpls.2017.01168

[…] if available., three genomic regions associated with cmd resistance have been recognized; cmd1 is a quantitative source of resistance identified in the amani derived interspecific variety tms 30572 (fregene, ; mohan et al., ), cmd2 is a region of large effect which has been widely used in iitas breeding program and has been mapped in several studies (akano et al., ; lokko et al., ; okogbenin et […]

PMCID: 5606945
PMID: 28707249
DOI: 10.1007/s00122-017-2943-z

[…] landrace tme3 (akano et al. ; rabbi et al. ), and a more quantitative source of cmd resistance called cmd1, derived from an amani interspecific cross, now known as tms 30572 (now tms-i30572) (fregene et al. ; mohan et al. ). a third putative source of resistance, known as cmd3, has also been described (okogbenin et al. ). novel sources and additional information on the genetic basis […]

PMCID: 5496946
PMID: 28725234
DOI: 10.3389/fpls.2017.01169

[…] sequence draft of cassava., the mapping population consists of 117 full sib f1 segregating population derived from a cross between nigerian cultivar tms30572 and ciat's elite cultivar cm2177-2 (fregene et al., ). this population has been used extensively in mapping studies (fregene et al., ; jorge et al., ; mba et al., ; lopez et al., ; soto et al., ). to produce multiple clonal plants […]

PMCID: 5426748
PMID: 28493955
DOI: 10.1371/journal.pone.0177456

[…] china represents mostly outbred offspring derived from parent plants from other countries., the population differential coefficients were lower than those of the 283 cassava samples calculated by fregene et al. [] and that of 36 african cassava land races reported by raji et al. []. this indicates that the 134 cassava germplasms used in our study are suitable for association mapping based […]

PMCID: 5021159
PMID: 26662210
DOI: 10.1111/mpp.12353

[…] programmes in africa (nichols, ). this mechanism was later found to be polygenic and recessive in nature (hahn et al., ), with the gene(s) conferring this resistance mapped and named as cmd1 (fregene and puonti‐kaerlas, ). cultivars possessing cmd1‐type resistance have been widely deployed in east and west africa, mostly as the tropical manihot species (tms) series (okogbenin et al., ) […]

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FREGENE institution(s)
Department of Epidemiology and Public Health, Imperial College, London, UK

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