GARD: A genetic algorithm for recombination detection

Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.
Bioinformatics (Impact Factor: 4.98). 01/2007; 22(24):3096-8. DOI: 10.1093/bioinformatics/btl474
Source: PubMed


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.
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Available from: Simon D W Frost
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    • "Sequences used for the comparison involved the following genotypes: HBoV1 (GenBank accession number NC_007455, DQ000496, DQ000495, KC823115), HBoV2 (NC_012042, GU301644, EU082214, FJ170278, GU048664), HBoV3 (EU918736, GU048665, FJ948861, FJ973562, HM132056, FJ973563, GQ867667), HBoV4 (KC461233, FJ973561), GBoV (HM145750), wild chimpanzee (HQ113148, HQ113146, HQ113151, HQ113150) and gorilla (HQ113149, HQ113147, HQ113145) isolates and canine minute virus as an outgroup (FJ899734). Detection of possible recombination breakpoints was performed using Simplot (Lole et al., 1999) and GARD (Kosakovsky Pond et al., 2006) software, only breakpoints supported by 70% of permutated trees were followed. P-distances were computed using PAUP software version 4b.10 (Swofford, 2002) "
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    • "The alignment was manually edited in Bioedit, version 7.05 to preserve frame insertions and deletions if present. Because recombination may confound the results of phylogeographic inference [Schierup and Hein, 2000], all data sets for phylogeographic analyses were verified and tested negative for recombination using RIP 3.0 [Siepel et al., 1995] and GARD [Pond et al., 2006]. The sequences of each subject have been submitted to GenBank (GenBank accession number: KP796426 -KP797835). "
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    • "which implements statistical tests associated with the programme HyPhy (Pond et al. 2005), was used to analyse an alignment of all unique haplotypes in the Welsh populations with the laboratory sequences downloaded from GenBank. We used GARD (Genetic Algorithm for Recombination Detection; Pond et al. 2006) to test for evidence for recombination prior to using tests of selection. We chose the best fitting substitution model using CodonTest (Delport et al. 2010), and then various codon-based tests for selection were implemented. "
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