ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes an...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-02-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1004041 |
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| _version_ | 1849726605968015360 |
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| author | Xavier Didelot Daniel J Wilson |
| author_facet | Xavier Didelot Daniel J Wilson |
| author_sort | Xavier Didelot |
| collection | DOAJ |
| description | Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. We find evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582. ClonalFrameML is freely available at http://clonalframeml.googlecode.com/. |
| format | Article |
| id | doaj-art-71e265fdb0eb4e998c6b6cce343c6878 |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2015-02-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-71e265fdb0eb4e998c6b6cce343c68782025-08-20T03:10:07ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582015-02-01112e100404110.1371/journal.pcbi.1004041ClonalFrameML: efficient inference of recombination in whole bacterial genomes.Xavier DidelotDaniel J WilsonRecombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. We find evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582. ClonalFrameML is freely available at http://clonalframeml.googlecode.com/.https://doi.org/10.1371/journal.pcbi.1004041 |
| spellingShingle | Xavier Didelot Daniel J Wilson ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Computational Biology |
| title | ClonalFrameML: efficient inference of recombination in whole bacterial genomes. |
| title_full | ClonalFrameML: efficient inference of recombination in whole bacterial genomes. |
| title_fullStr | ClonalFrameML: efficient inference of recombination in whole bacterial genomes. |
| title_full_unstemmed | ClonalFrameML: efficient inference of recombination in whole bacterial genomes. |
| title_short | ClonalFrameML: efficient inference of recombination in whole bacterial genomes. |
| title_sort | clonalframeml efficient inference of recombination in whole bacterial genomes |
| url | https://doi.org/10.1371/journal.pcbi.1004041 |
| work_keys_str_mv | AT xavierdidelot clonalframemlefficientinferenceofrecombinationinwholebacterialgenomes AT danieljwilson clonalframemlefficientinferenceofrecombinationinwholebacterialgenomes |