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ClonalOrigin specifications


Unique identifier OMICS_18881
Name ClonalOrigin
Software type Framework/Library, Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes




No version available


  • person_outline Xavier Didelot

Additional information

Publication for ClonalOrigin

ClonalOrigin citations


Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades

Mol Biol Evol
PMCID: 5913663
PMID: 29688542
DOI: 10.1093/molbev/msy027

[…] an underestimation of recombination events and thus in an overestimation of the substitution rate. In addition, methods based on the assumption that all isolates were sampled at the same time [e.g., ClonalOrigin (), BratNextGen ()] are not applicable.Alignments were masked from recombination by masking recombinant stretches detected by ClonalFrameML. Thereby, recombinant stretches on terminal lin […]


Genomic divergence and cohesion in a species of pelagic freshwater bacteria

BMC Genomics
PMCID: 5644125
PMID: 29037158
DOI: 10.1186/s12864-017-4199-z
call_split See protocol

[…] man-Rubin convergence test []. By comparing the output trees it was verified that the three runs produced a consistent genealogy. Based on this genealogy, further properties of HR were inferred using ClonalOrigin [], which performs approximate inference under the coalescent model with gene conversion []. ClonalOrigin infers the origin and destination of recombination events on the genealogy, as we […]


A Locus Encoding Variable Defense Systems against Invading DNA Identified in Streptococcus suis

Genome Biol Evol
PMCID: 5398294
PMID: 28379509
DOI: 10.1093/gbe/evx062

[…] yses must be performed with a large number of strains, including the quantification of horizontal transfer and homologous recombination in each genomic cluster by using programs such as GUBBINS () or CLONALORIGIN (). In this study, several loci that shift defense elements were revealed through comprehensive analyses of the defense elements and their locations. The variable region of defense elemen […]


gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances

PLoS One
PMCID: 5112998
PMID: 27846272
DOI: 10.1371/journal.pone.0166602

[…] is also a group of programs based on statistical or probabilistic methods for modeling recombination events between bacterial genomes, e.g., RDP4 [], BratNextGen [], ClonalFrame [], ClonalFrameML [], ClonalOrigin [], fineSTRUCTURE [], and orderedPainting []. However, these methods typically handle only a subset of genomic loci, since the analysis of complete genomes is hindered by computationally […]


Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak

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

[…] croevolution implemented in ClonalFrame []. Genomes were aligned using progressiveMauve [] and collinear blocks bigger than 500 bp were filtered using the perl script stripSubsetLCBs available in the ClonalOrigin package []. Thus, ClonalFrame was run with 10,000 burn-in iterations followed by 10,000 data collection iterations. The consensus tree represents combined data from three independent runs […]


Evolution and Comparative Genomics of Campylobacter jejuni ST 677 Clonal Complex

Genome Biol Evol
PMCID: 4202330
PMID: 25193305
DOI: 10.1093/gbe/evu194

[…] lution implemented in ClonalFrame (). The contigs were aligned using progressive Mauve (), and collinear blocks bigger than 500 bp were filtered using the perl script stripSubsetLCBs available in the ClonalOrigin package (). ClonalFrame was run with 10,000 burn-in iterations followed by 10,000 data collection iterations. The strict (100%) consensus tree represents combined data from three independ […]


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ClonalOrigin institution(s)
Department of Statistics, University of Oxford, Oxford, UK; Department of Mathematics, University of Bristol, Bristol, United Kingdom; Genome Center, University of California, Davis, CA, USA; Environmental Research Institute, University College, Cork, Ireland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
ClonalOrigin funding source(s)
Supported by Wellcome Trust grant WT082930MA, National Science Foundation grant DBI-0630765, Science Foundation of Ireland grant 05/FE1/B882.

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