ClonalFrame protocols

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ClonalFrame specifications

Information


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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Documentation


Maintainer


  • person_outline Xavier Didelot <>

Additional information


A version called ClonalFrameML is available for bacterial genome at https://github.com/xavierdidelot/clonalframeml

Publications for ClonalFrame

ClonalFrame in pipelines

 (19)
2018
PMCID: 5862964
PMID: 29563494
DOI: 10.1038/s41467-018-03205-z

[…] 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 […]

2017
PMCID: 5635113
PMID: 29018197
DOI: 10.1038/s41467-017-00808-w

[…] with poorly populated spots. the diversity was computed per clade for each of the concatenates., we inferred homologous recombination on the multiple alignments of the core genes of each clade using clonalframeml (cfml) v10.7.5 with a predefined tree (i.e., the clade’s tree), default priors r/θ = 10−1, 1/δ = 10−3, and ν = 10−1, and 100 pseudo-bootstrap replicates, as previously suggested. mean […]

2016
PMCID: 4792440
PMID: 26978068
DOI: 10.1371/journal.pone.0151240

[…] defined in all isolates by comparison to the annotated genome of s. epidermidis rp62a []. reciprocal best hits identifying 11,168 rps and rpl alleles were identified using blast as described above. clonalframe, a model-based approach to determining microevolution in bacteria, was used to estimate the genealogies for these alignments []. this program differentiates mutation and recombination […]

2016
PMCID: 5025774
PMID: 27633769
DOI: 10.1038/srep33442

[…] alignment of 759,392 nucleotides of the 1140 protein-coding genes (), the ml phylogeny of the concatenated alignment of 299,244 amino acid residues of the 1140 translated core genes (), and a clonalframe nucleotide-based phylogenetic analysis. the latter has the advantage of removing most recombinant regions of the dna alignment from consideration. all three approaches yielded similar […]

2015
PMCID: 4489044
PMID: 25887605
DOI: 10.1186/s12864-015-1377-8

[…] the program readal []. the phylogenetic tree was used as input for splitstree4. in order to identify recombination hotspots, the analysis was repeated using fragments of the genome. additionally, clonalframe [], another program to test for recombination, was applied to the multiple genome alignment produced by mauve., additional file 1: additional file 2: additional file 3: […]


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ClonalFrame in publications

 (197)
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] from 14 gull and 12 bald eagle faecal samples was further analysed., 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 […]

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

[…] 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). […]

PMCID: 5928088
PMID: 29712985
DOI: 10.1038/s41598-018-25233-x

[…] from the annotated whole-genome sequence of the 33 strains. ribosomal protein l36 and l31 type b gene was excluded from the analysis because of the presence of paralogues in some genomes. a clonalframe tree (fig. ) was inferred from the 53 concatenated ribosomal protein gene sequences that are single-copy and shared by the 33 strains, which revealed that the novel stx2h converting […]

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

[…] of 133 genomes from the pubmlst neisseria genome database representing all major invasive disease lineages in some of these phylogenetic analyses as references., we assessed recombination by using clonalframeml and gubbins (,). we then mapped the recombination to the cc4821 reference genome 053442 (online technical appendix)., we assessed gene content by using the roary 3.6 ortholog clustering […]

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

[…] 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 […]


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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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