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GARD specifications


Unique identifier OMICS_30553
Alternative name Genetic Algorithm for Recombination Detection
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Genetic Algorithm for Recombination Detection

GARD citations


Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV

Front Microbiol
PMCID: 5938362
PMID: 29765366
DOI: 10.3389/fmicb.2018.00854

[…] ence alignment as a scaffold for constructing the corresponding DNA multiple alignment. All alignments were screened for the presence of recombination using Genetic Algorithm Recombination Detection (GARD) () and two methods (RDP and GENECONV) (; ) implemented in the RDP4 program (). RDP and GENECONV were selected because they showed good power in previous simulation analyses (; ) and only breakpo […]


Full Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus

PMCID: 5923487
PMID: 29652824
DOI: 10.3390/v10040193
call_split See protocol

[…] so performed to confirm these putative recombination events. The occurrence of recombination in BAGV genomes was also investigated with a method called Genetic Algorithms for Recombination Detection (GARD) implemented in Datamonkey web server ( [], that estimates breakpoints based on a genetic algorithm. The statistical significance of putative breakpoints was evaluated throu […]


UDP glycosyltransferase genes in trypanosomatid genomes have diversified independently to meet the distinct developmental needs of parasite adaptations

BMC Evol Biol
PMCID: 5853035
PMID: 29540192
DOI: 10.1186/s12862-018-1149-6

[…] of recombination and subsequently performed six tests of site-level selection. Three tests found evidence for recombination among T. congolense genes with three significant breakpoints identified by GARD taking into account rate variation. The six tests for positive selection performed did not show evidence for positive selected sites; only PAML identified one site under positive selection at nuc […]


Ancient Evolution of Mammarenaviruses: Adaptation via Changes in the L Protein and No Evidence for Host–Virus Codivergence

Genome Biol Evol
PMCID: 5863214
PMID: 29608723
DOI: 10.1093/gbe/evy050
call_split See protocol

[…] llows the automated removal of poorly aligned codons from a multiple sequence alignment (), for filtering codons with a score <0.90 ().Alignments were screened for the presence of recombination using GARD (), a genetic algorithm from the HYPHY suite. GARD is based on the concept that recombination results in regions having different evolutionary histories and thus uses phylogenetic incongruence am […]


Circulatory white spot syndrome virus in South West region of Bangladesh from 2014 to 2017: molecular characterization and genetic variation

PMCID: 5818386
PMID: 29460184
DOI: 10.1186/s13568-018-0553-z

[…] RDP and GARD based recombination detection methods implemented in this study showed no breakpoint event and hence recombination in VP28 sequences along with out-group [Monodon Baculovirus (MBV)] included for […]


Origin and dispersal of Hepatitis E virus

PMCID: 5837148
PMID: 29410449
DOI: 10.1038/s41426-017-0009-6
call_split See protocol

[…] es was generated using MAFFT. The region corresponding to the hypervariable region (HVR) was filtered due to very poor alignment quality and recombination was searched for using the genetic algorithm GARD implemented in the HYPHY package. GARD uses phylogenetic incongruence among segments in an alignment to detect the best-fit number and location of recombination breakpoints and evaluates the stat […]


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GARD institution(s)
Department of Pathology, University of California San Diego, San Diego, CA, USA; University of Vigo, Vigo, Spain; School of Medicine, University of Swansea, Swansea, UK
GARD funding source(s)
Supported in part by the National Institutes of Health (AI43638, AI47745, and AI57167), the University of California Universitywide AIDS Research Program (grant number IS02-SD-701), and by a University of California, San Diego Center for AIDS Research/ NIAID Developmental Award (AI36214); by grant R01-GM66276 from the US National Institutes of Health, grant BFU2004-02700 of the Spanish Ministry of Education and Science, and the ‘‘Ramon y Cajal’’ programme of the Spanish government.

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