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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
C++ compiler, R, ape, phangorn
Maintained Yes




No version available



  • person_outline Xavier Didelot

Additional information

A version called ClonalFrameML is available for bacterial genome at

Publications for ClonalFrame

ClonalFrame citations


Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] The maximum likelihood phylogeny based on the core genome (i.e. orthologous regions present in all genomes), and estimated using ClonalFrameML to account for mutation and recombination events, revealed a diverse population of E. coli isolates (Fig. ). All four major E. coli phylotypes were identified through in silico phylotypi […]


Invasive Methicillin Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages

PMCID: 5932375
PMID: 29720528
DOI: 10.1128/mSphere.00571-17
call_split See protocol

[…] 539 CC8 strains from this study and 24 CC8 strains described in other papers was processed using Parsnp (). The alignment length was 2,361,133 bp. Potential recombination sites were identified using ClonalFrameML () based on a maximum likelihood (ML) guide tree constructed by PhyML (, ), removed using a custom R script, leaving a final alignment of 2,359,393 bp with 18,755 variable sites (SNPs). […]


Identification and pathogenomic analysis of an Escherichia coli strain producing a novel Shiga toxin 2 subtype

Sci Rep
PMCID: 5928088
PMID: 29712985
DOI: 10.1038/s41598-018-25233-x
call_split See protocol

[…] ocus typing (wgMLST). The ribosomal protein subunites (rps) gene sequences were extracted from the annotated whole-genome sequence of the 33 strains. Three independent runs were then carried out with ClonalFrame (version 1.2) on the extracted rps gene sequences and the outputs of the analyses were converged and merged to generate a 95% consensus tree. For wgMLST analysis, the completed whole-genom […]


Evolution of Sequence Type 4821 Clonal Complex Meningococcal Strains in China from Prequinolone to Quinolone Era, 1972–2013

PMCID: 5875256
PMID: 29553310
DOI: 10.3201/eid2404.171744

[…] We identified extensive recombination within CC4821 lineage, as detected by ClonalFrameML (). The estimated rate of recombination relative to mutation (R/ϴ) for the entire CC4821 core genome was 1.37 (95% CI 1.40–1.34), and the relative impact of recombination to mutation (r/ […]


Vancomycin resistant Enterococcus faecium sequence type 796 rapid international dissemination of a new epidemic clone

PMCID: 5863837
PMID: 29588851
DOI: 10.1186/s13756-018-0335-z
call_split See protocol

[…] ive of the ST796 lineage []. Single nucleotide polymorphisms (SNPs) in core genome positions were used to construct a Maximum Likelihood tree with FastTree v2.1.8 []. The tree was used as a guide for ClonalFrame v1.7 to infer regions of recombination []. As previously described, a robust and recombination-free tree was generated []. Tree branches with less than 70% bootstrap support (500 replicate […]


The global distribution and spread of the mobilized colistin resistance gene mcr 1

Nat Commun
PMCID: 5862964
PMID: 29563494
DOI: 10.1038/s41467-018-03205-z

[…] cting the transposon phylogeny, we excluded the downstream ISApl1 and the insertion sequence observed in a small number of samples, as well as regions identified as having signals of recombination by ClonalFrameML, resulting in a 3522 bp alignment. We removed two homoplastic sites (requiring >1 change on the phylogeny), before constructing a maximum parsimony neighbor-joining tree based on the Ham […]


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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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