ClonalFrame pipeline

ClonalFrame specifications


Unique identifier OMICS_14623
Name ClonalFrame
Alternative name ClonalFrameML
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2
Stability Stable
Requirements C++ compiler, R, ape, phangorn
Maintained Yes



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  • person_outline Xavier Didelot <>

Additional information

A version called ClonalFrameML is available for bacterial genome at

Publications for ClonalFrame

ClonalFrame IN pipelines

PMCID: 4449606
PMID: 25880915
DOI: 10.1186/s12864-015-1476-6

[…] in the “bifido” group (1.8%)., finally, we quantified the overall ratio at which recombination and mutation events (r/m) have generated substitutions in the strains sequenced here. to this end, clonalframe was run on genes previously used in multilocus sequence typing of lactobacillus casei (fusa, iles, leus, pyrg, reca and recg) and bifidobacterium spp. (fusa, iles, gyrb, rplb and rpob). […]

PMCID: 4552844
PMID: 26317849
DOI: 10.1371/journal.pone.0134592

[…] variant (slv) of the primary founder may diversify to produce multiple slvs and this was denoted a subgroup founder., the population-scaled mutation and recombination parameters were estimated using clonalframe v1.2 [20]. the concatenated nucleotide sequence of each of the seven mlst loci were used as input and a single representative of each st was used in order to minimize bias resulting […]

PMCID: 4168118
PMID: 25196593
DOI: 10.1186/1471-2164-15-768

[…] by genetic drift, allowing us to estimate the distance between c. jejuni 4031 and ihv116292, assuming that similar pfge patterns originated from a common ancestor. the genealogy reconstructed using clonalframe based on core genome alignment obtained with progressivemauve is presented in figure 3. the tree shows a monophyletic relationship between c. jejuni 4031, the human isolate ihv116260 […]

PMCID: 3846478
PMID: 24312460
DOI: 10.1371/journal.pone.0080175

[…] selection; dn/ds>1, positive selection [38]. the relative impact of homologous recombination on the variation of the b. cereus s.l. populations was estimated by calculation of the r/m ratio using clonalframe software version 1.2 [39]. the analysis was performed on the complete dataset (n = 273) and with regard to each environment with four independent runs. the basis of 100,000 iterations […]

ClonalFrame institution(s)
Department of Infectious Disease Epidemiology, Imperial College, London, UK; Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; Wellcome Trust Centre for Human Genetics, Oxford, UK
ClonalFrame funding source(s)
This work was supported by the National Institute for Health Research through Health Protection Research Unit funding, a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (Grant 101237/Z/13/Z), the Oxford NIHR Biomedical Research Centre, the UKCRC Modernising Medical Microbiology Consortium, the UKCRC Translational Infection Research Initiative supported by the Medical Research Council, the Biotechnology and Biological Sciences Research Council and the National Institute for Health Research on behalf of the UK Department of Health (Grant G0800778) and the Wellcome Trust (Grant 087646/Z/08/Z).

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