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Citations per year

Number of citations per year for the bioinformatics software tool GiRaF
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This map represents all the scientific publications referring to GiRaF per scientific context
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Protocols

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 citations

 (9)
library_books

Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses

2017
Microb Genom
PMCID: 5857367
PMID: 29310750
DOI: 10.1099/mgen.0.000137

[…] ther inter-subgroup reassortment event. With these 11 reassortment events, the rate of inter-subgroup reassortment is estimated to be 7.3 %.Eight of these reassortment events were also detected using GiRaF, an automated reassortment detection tool (the rate of inter-subgroup reassortment is reduced to 5.3 % if only these events are considered). Of the remaining three reassortment events (samples 1 […]

library_books

Frequency of influenza H3N2 intra subtype reassortment: attributes and implications of reassortant spread

2016
BMC Biol
PMCID: 5200972
PMID: 28034300
DOI: 10.1186/s12915-016-0337-3

[…] assortment events by the total number of influenza genomes, we estimated the frequency of H3N2 intra-subtype reassortment (during years 2008–2014) for both the 20 smaller data subsets used in MrBayes/GiRaF (MCMC) analyses, and for the full dataset derived by combined MCMC and ML analyses. The average frequency of reassortment events in the smaller data subsets was comparable to the frequency of th […]

call_split

Reassortment compatibility between PB1, PB2, and HA genes of the two influenza B virus lineages in mammalian cells

2016
Sci Rep
PMCID: 4897687
PMID: 27270757
DOI: 10.1038/srep27480
call_split See protocol

[…] 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 (G […]

call_split

Coordinated Evolution of Influenza A Surface Proteins

2015
PLoS Genet
PMCID: 4527594
PMID: 26247472
DOI: 10.1371/journal.pgen.1005404
call_split See protocol

[…] We used GiRaF [] to identify sets of taxa that are descendant to reassortment events. To reduce the computational burden associated with this step, we first clustered isolates with nucleotide identity exceedi […]

call_split

Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes

2014
PLoS Genet
PMCID: 3886890
PMID: 24415946
DOI: 10.1371/journal.pgen.1004037
call_split See protocol

[…] genetic mapping of reassortments, we used a two-step procedure. First, we computationally predicted the subsets of taxa that occupied incompatible positions in phylogenies of different segments using GIRAF software running on a cluster node with 512 Gb of RAM. GiRaF automatically predicted the subsets of taxa originating from each ancestral reassortment event on the basis of the MrBayes sampled t […]

library_books

Molecular Evolution of Zika Virus during Its Emergence in the 20th Century

2014
PLoS Negl Trop Dis
PMCID: 3888466
PMID: 24421913
DOI: 10.1371/journal.pntd.0002636

[…] data. This is in line with the use of Maximum Likelihood approaches, which is fairly robust to the introduction of gaps , . In addition, we found incompatibilities between E and NS5 phylogenies using GiRaF. The three discordant strains (ArD128000, ArA1465 and ArD142623) were excluded, and we used 40 (31 from E and 36 from NS5) concatenated sequences for phylogenetic analysis. Moreover, we also fou […]


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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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