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Gingr specifications


Unique identifier OMICS_21462
Name Gingr
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input format MultiFASTA, Newick, VCF, Genbank, XMFA, MAF
Output format Newick, MultiFASTA (SNPs only), VCF, XMFA
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Medium
Version 1.2
Stability Stable
gcc compiler
Maintained Yes




No version available



  • person_outline Todd J. Treangen <>

Publication for Gingr

Gingr citations


Short genome report of cellulose producing commensal Escherichia coli 1094

PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] posterior nj (neighbor joining) phylogenetic reconstruction was carried out with parsnp, a fast core-genome multi-aligner, using default parameters []. alignment and tree visualization was done with gingr, a dynamic visual platform (fig. ) []., we selected five e. coli genomes that are representative of the multiple clades within phylogenetic group a, and performed orthologous clustering […]


Invasive Methicillin Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages

PMCID: 5932375
PMID: 29720528
DOI: 10.1128/mSphere.00571-17

[…] in subgroups a to f when we included a more divergent st630 in a pilot phylogeny. one strain in group f, ct-172, was pruned from the final tree because of a long branch. visual inspection using the gingr tool () revealed the presence of a likely large recombinant region in this strain between 2.47 and 2.59 mbp on the usa500-2395 reference coordinates that had not been detected […]


The impact of serotype specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan genome

PMCID: 5902063
PMID: 29617440
DOI: 10.1371/journal.ppat.1006966

[…] age groups to 10,000 random deviates of a dirichlet distribution []., a subsample of isolates from each sc and 25 publicly available reference genomes were aligned using parsnp and visualized using gingr to identify the most appropriate genome for reference-based mapping []. the phylogenetically closest genome was selected for reference-based mapping of isolates belonging to that sc. for four […]


Genetic Analysis of Virulence Potential of Escherichia coli O104 Serotypes Isolated From Cattle Feces Using Whole Genome Sequencing

PMCID: 5838399
PMID: 29545780
DOI: 10.3389/fmicb.2018.00341

[…] were determined in silico using mlst 1.8 ( (wirth et al., ; jaureguy et al., ). the harvest suite, a software package which includes tools such as parsnp and gingr, was used to determine the phylogenetic relationship among the e. coli o104 strains (treangen et al., ). parsnp v1.2 ( was used […]


Genome analysis of clinical multilocus sequence Type 11 Klebsiella pneumoniae from China

PMCID: 5857376
PMID: 29424684
DOI: 10.1099/mgen.0.000149

[…] and virulence determinants were generated using an in-house script., the harvest suite, which was designated for analyzing intraspecific microbial genomes and encompasses three modules (parsnp, gingr and harvesttools), was applied to filter recombination (-x), run core genome alignment and variant calling and reconstruct the phylogenetic tree with the 58 assembled genomes using default […]


Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

PMCID: 5801463
PMID: 29437920
DOI: 10.1128/mBio.02011-17

[…] all snps required a read depth of ≥10 reads with ≥90% of those aligned reads supporting the variant nucleotide call. core genome alignments were performed by using parsnp and visualized by using gingr ()., plasmid detection in shotgun assemblies was determined by using a k-mer inclusion approach. briefly, 16-bp k-mers were generated from the fully resolved pacbio plasmid sequences along […]

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Gingr institution(s)
National Biodefense Analysis and Countermeasures Center, MD, USA
Gingr funding source(s)
Supported by an Agreement (No. HSHQDC-07-C-00020) awarded by the Department of Homeland Security Science and Technology Directorate (DHS/S&T) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC); and a Federally Funded Research and Development Center.

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