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inference of bacterial microevolution using multilocus sequence data

ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, we recommend using Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.




LicenseVerified byVerified onNotes
GPLv2orlaterDebian20 March 2013
License: GPL-2+

GPL-2+ ClonalFrame is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

ClonalFrame is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with Velvet; if not, write to the Free Software Foundation,

Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
PublicDomainDebian20 March 2013
License: PD

PD The packaging work is in the public domain unless stated


Leaders and contributors

Xavier Didelot contact

Resources and communication

AudienceResource typeURI

Software prerequisites


Date 2013-03-20
Source Debian import
Source link


"contact" is not in the list (Maintainer, Contributor, Developer, Sponsor, Unknown) of allowed values for the "Role" property.

Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.

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