ClonalFrame protocols

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



Add your version



  • person_outline Xavier Didelot <>

Additional information

A version called ClonalFrameML is available for bacterial genome at

Publications for ClonalFrame

ClonalFrame IN pipelines

PMCID: 5025774
PMID: 27633769
DOI: 10.1038/srep33442

[…] nucleotides of the 1140 protein-coding genes (fig. 1), the ml phylogeny of the concatenated alignment of 299,244 amino acid residues of the 1140 translated core genes (supplementary figure 1), and a clonalframe nucleotide-based phylogenetic analysis23. the latter has the advantage of removing most recombinant regions of the dna alignment from consideration. all three approaches yielded similar […]

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

[…] the cc97 isolates were more closely related to st71 than st97., to examine the role of recombination on s. aureus population structure, the concatenated mlst nucleotide sequences were analysed using clonalframe. the mean recombination tract length (δ) was estimated to be 152 bp (95% confidence interval 11–850 bp). the estimate of the rate at which nucleotides change by recombination versus point […]

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: 4161309
PMID: 25210772
DOI: 10.1371/journal.pgen.1004596

[…] for this analysis, genomic regions were aligned with clustalw as implemented in geneious r6 and stripped from all alignment gaps. to calculate the r/m ratios, two independent runs with the program clonalframe [94] were performed on orthologs shared between sags and reference genomes from a. mellifera. each run consisted of 100,000 iterations, with a burn-in of 50,000 iterations. parameters […]

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).

ClonalFrame reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ClonalFrame