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GiRaF specifications

Information


Unique identifier OMICS_29113
Name GiRaF
Alternative name Graph-incompatibility-based Reassortment Finder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.02
Stability Stable
Maintained Yes

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Publication for Graph-incompatibility-based Reassortment Finder

GiRaF in publications

 (14)
PMCID: 5857367
PMID: 29310750
DOI: 10.1099/mgen.0.000137

[…] the rate of reassortment was estimated by dividing the number of reassortment events by the total number of viruses. phylogenetic mapping of reassortants was also performed computationally using the graph-incompatibility-based reassortment finder (giraf) software v1.02 []. posterior samples of phylogenies generated for each segment using beast were thinned (downsampled) to 1000 trees […]

PMCID: 5338237
PMID: 27327045
DOI: 10.1002/pro.2971

[…] indicating that π–π interactions are favored., we searched binding sites that are similar to the nvp binding sites in 1vrt, by using two existing binding site similarity search engines, ef‐seek, giraf, and probis. however, 2hmk is not detected by these methods (this entry was found in neither top‐100 similar binding sites in ef‐seek and giraf, and the z‐score ≥1.0 hit list in probis). since […]

PMCID: 4897687
PMID: 27270757
DOI: 10.1038/srep27480

[…] obtained from the mcmc tree samples using treeannotator v1.8.2 and were visualized using fig tree (v1.4.2) (http://tree.bio.ed.ac.uk/software/figtree/)., reassortment events were analyzed using the graph incompatibility-based reassortment finder (giraf) program. aligned nucleotide sequence sets of the eight genetic segments were used for the phylogenetic relationship reconstruction in mrbayes […]

PMCID: 4527594
PMID: 26247472
DOI: 10.1371/journal.pgen.1005404

[…] the two surface proteins ha and na for the two major influenza subtypes circulating in humans, h3n2 and h1n1. as expected, ha and na phylogenies of the same subtype were incongruent. using software giraf [], we identified taxa that descended from within-subtype reassortant ancestors and thus inferred the positions of reassortment events on the phylogenies of an individual segment (see […]

PMCID: 3888466
PMID: 24421913
DOI: 10.1371/journal.pntd.0002636

[…] potential intra-gene recombination was also inspected with rdp using individual gene datasets, and the incompatibility among phylogenies inferred from genes (ns5 and e) was also investigated with giraf v1.01 that searches incompatible clades among posterior set of trees (pst) obtained from different genomic regions with threshold of 70% for incompatible clades. the pst was obtained […]


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GiRaF institution(s)
Computational and Mathematical Biology, Genome Institute of Singapore, Singapore; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Computer Science, University of Maryland, College Park, MD, USA
GiRaF funding source(s)
Supported by National Science Foundation (EF-0849899 and IIS-0812111); the National Institutes of Health (1R21AI085376).

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