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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


No version available

Publication for FREGENE

FREGENE citations


cophesim: a comprehensive phenotype simulator for testing novel association methods

PMCID: 5605948
PMID: 28979766
DOI: 10.5256/f1000research.12938.r24718

[…] a, which may not be easily obtainable. One solution is to use artificial data simulated with specific assumptions.The best existing phenotype simulators, such as: GENOME , Plink , phenosim , CoaSim , Fregene , ForSim , QuantiNemo , GCTA , HapGen , SeqSimla , and SimRare offer qualitative and dichotomous simulated phenotype. But the known phenotype simulation software tools have some limitations, […]


QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii

Front Plant Sci
PMCID: 5519584
PMID: 28785268
DOI: 10.3389/fpls.2017.01168

[…] s, 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 a […]


QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi parental cross of two Tanzanian farmer varieties, Namikonga and Albert

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

[…] egregation in Namikonga facilitates segregation in F1 which is the generation at which most cassava breeders do selections.To date, three loci associated with CMD resistance have been reported: CMD1 (Fregene et al. ), CMD2 (Akano et al. ; Lokko et al. ; Rabbi et al. ), and CMD3 (Okogbenin et al. ). The CMD2 locus was identified in West African cassava landraces TME3 and TME7 (now TMEB3 and TMEB7, […]


Major Novel QTL for Resistance to Cassava Bacterial Blight Identified through a Multi Environmental Analysis

Front Plant Sci
PMCID: 5496946
PMID: 28725234
DOI: 10.3389/fpls.2017.01169

[…] ants estimated in this study was 20 and 53% for resistance to Xam318 and Xam681, respectively. The values are in the range of the previously reported studies of 10–69% (Hahn et al., ; Jorge et al., ; Fregene et al., ; Ly et al., ). These values of heritability highlight the important effect of the environmental conditions on plant response to CBB. In particular, the humidity showed a strong influe […]


Molecular diversity analysis, drought related marker traits association mapping and discovery of excellent alleles for 100 day old plants by EST SSRs in cassava germplasms (Manihot esculenta Cranz)

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

[…] from 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 on l […]


Cassava Breeding I: The Value of Breeding Value

Front Plant Sci
PMCID: 5003041
PMID: 27621734
DOI: 10.3389/fpls.2016.01227

[…] y (Restrepo and Verdier, ; Hernández Pérez et al., ; Monger et al., ,; Álvarez et al., , ; Calvert et al., ; Legg et al., ); gene expression studies in host-pathogen interactions (Hong and Stanley, ; Fregene et al., ; Kemp et al., , ); introgression of resistance to cassava mosaic disease (CMD) in Latin American germplasm (Egesi et al., ; Okogbenin et al., ), or dissection of the pathway leading t […]


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

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