GARD: a genetic algorithm for recombination detection
Motivation: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic t...
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| Published in | Bioinformatics Vol. 22; no. 24; pp. 3096 - 3098 |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Oxford University Press
15.12.2006
Oxford Publishing Limited (England) |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1460-2059 1367-4811 |
| DOI | 10.1093/bioinformatics/btl474 |
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| Abstract | Motivation: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments. Results: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection. Availability: Freely available Contact:spond@ucsd.edu |
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| AbstractList | Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments.MOTIVATIONPhylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments.We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection.RESULTSWe developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection.Freely available http://www.datamonkey.org/GARD/AVAILABILITYFreely available http://www.datamonkey.org/GARD/ Motivation: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments. Results: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection. Availability: Freely available Contact:spond@ucsd.edu MOTIVATION: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments. RESULTS: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection. AVAILABILITY: Freely available http://www.datamonkey.org/GARD/ CONTACT: spond super(c)sd.edu Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments. We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection. Freely available http://www.datamonkey.org/GARD/ Motivation: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments. Results: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection. Availability: Freely available http://www.datamonkey.org/GARD/ Contact: spond@ucsd.edu Motivation: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments. Results: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection. Availability: Freely available Contact: spond@ucsd.edu |
| Author | Posada, David Kosakovsky Pond, Sergei L. Gravenor, Michael B. Frost, Simon D.W. Woelk, Christopher H. |
| Author_xml | – sequence: 1 givenname: Sergei L. surname: Kosakovsky Pond fullname: Kosakovsky Pond, Sergei L. organization: Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA, Facultad de Biología, Universidad de Vigo, Vigo 36310, Spain, Swansea, UK – sequence: 2 givenname: David surname: Posada fullname: Posada, David organization: Departamento de Bioquímica, Genética e InmunologíaFacultad de Biología, Universidad de Vigo, Vigo 36310, Spain – sequence: 3 givenname: Michael B. surname: Gravenor fullname: Gravenor, Michael B. organization: School of Medicine, University of WalesSwansea, UK – sequence: 4 givenname: Christopher H. surname: Woelk fullname: Woelk, Christopher H. organization: Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA, Facultad de Biología, Universidad de Vigo, Vigo 36310, Spain, Swansea, UK – sequence: 5 givenname: Simon D.W. surname: Frost fullname: Frost, Simon D.W. organization: Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA, Facultad de Biología, Universidad de Vigo, Vigo 36310, Spain, Swansea, UK |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18401841$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/17110367$$D View this record in MEDLINE/PubMed |
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| CODEN | BOINFP |
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| Cites_doi | 10.1073/pnas.241370698 10.1093/molbev/msl051 10.1128/JVI.76.22.11273-11282.2002 10.1093/oxfordjournals.molbev.a004129 10.1017/S0016672303006128 10.1093/oxfordjournals.molbev.a026256 10.1093/bioinformatics/bti079 10.1080/03610927808827599 10.1093/bioinformatics/bti320 10.1007/s00239-001-0034-9 |
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| Issue | 24 |
| Keywords | Breakpoint Recombination Multiple Genetic algorithm Sequence alignment Evolution Phylogeny Detection Bioinformatics Algorithm Scope note Comparative study |
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| References | Schierup (2023012408505604500_b8) 2000; 17 Shriner (2023012408505604500_b9) 2003; 81 Sugiura (2023012408505604500_b10) 1978; A7 Eshelman (2023012408505604500_b1) 1991 Kosakovsky Pond (2023012408505604500_b3) 2005; 21 Kosakovsky Pond (2023012408505604500_b2) 2005; 21 Posada (2023012408505604500_b5) 2001; 98 Zhuang (2023012408505604500_b11) 2002; 76 Posada (2023012408505604500_b6) 2002; 54 Posada (2023012408505604500_b7) 2002; 19 Kosakovsky Pond (2023012408505604500_b4) 2006; 23 |
| References_xml | – volume: 98 start-page: 13757 year: 2001 ident: 2023012408505604500_b5 article-title: Evaluation of methods for detecting recombination from DNA sequences: computer simulations publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.241370698 – volume: 23 start-page: 1891 year: 2006 ident: 2023012408505604500_b4 article-title: Automated phylogenetic detection of recombination using a genetic algorithm publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msl051 – volume: 76 start-page: 11273 year: 2002 ident: 2023012408505604500_b11 article-title: Human immunodeficiency virus type 1 recombination: rate, fidelity, and putative hot spots publication-title: J. Virol. doi: 10.1128/JVI.76.22.11273-11282.2002 – volume: 19 start-page: 708 year: 2002 ident: 2023012408505604500_b7 article-title: Evaluation of methods for detecting recombination from DNA sequences: empirical data publication-title: Mol. Biol. Evol. doi: 10.1093/oxfordjournals.molbev.a004129 – volume: 81 start-page: 115 year: 2003 ident: 2023012408505604500_b9 article-title: Potential impact of recombination on sitewise approaches for detecting positive natural selection publication-title: Genet. Res. doi: 10.1017/S0016672303006128 – volume: 17 start-page: 1578 year: 2000 ident: 2023012408505604500_b8 article-title: Recombination and the molecular clock publication-title: Mol. Biol. Evol. doi: 10.1093/oxfordjournals.molbev.a026256 – volume: 21 start-page: 676 year: 2005 ident: 2023012408505604500_b3 article-title: HyPhy: Hypothesis testing using phylogenies publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti079 – volume: A7 start-page: 13 year: 1978 ident: 2023012408505604500_b10 article-title: Further analysis of the data by Akaike's information criterion and the finite corrections publication-title: Comm. Stat. Theory Meth. doi: 10.1080/03610927808827599 – volume: 21 start-page: 2531 year: 2005 ident: 2023012408505604500_b2 article-title: Datamonkey: rapid detection of selective pressure on individual sites of codon alignments publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti320 – start-page: 265 volume-title: Foundations of Genetic Algorithms year: 1991 ident: 2023012408505604500_b1 article-title: The CHC adaptive search algorithm: How to do safe search when engaging in nontraditional genetic recombination – volume: 54 start-page: 396 year: 2002 ident: 2023012408505604500_b6 article-title: The effect of recombination on the accuracy of phylogeny estimation publication-title: J. Mol. Evol. doi: 10.1007/s00239-001-0034-9 |
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| Snippet | Motivation: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential... Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component... MOTIVATION: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential... |
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| SubjectTerms | Algorithms Base Sequence Biological and medical sciences Chromosome Mapping - methods Comparative studies Computer Simulation Conserved Sequence - genetics Evolution, Molecular Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Genetic Molecular Sequence Data Recombination, Genetic - genetics Sequence Alignment - methods Sequence Analysis, DNA - methods Sequence Homology, Nucleic Acid Software |
| Title | GARD: a genetic algorithm for recombination detection |
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