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



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  • person_outline Todd J. Treangen <>

Publication for Gingr

Gingr in publications

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 […]

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 […]

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 […]

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 […]

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 […]

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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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