Gingr specifications

Information


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
Requirements
gcc compiler
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Todd J. Treangen <>

Publication for Gingr

Gingr in publications

 (21)
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 (https://cge.cbs.dtu.dk/services/mlst/) (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 (http://harvest.readthedocs.io/en/latest/content/parsnp.html) 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

Gingr reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Gingr