GenGIS protocols

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GenGIS specifications

Information


Unique identifier OMICS_04013
Name GenGIS
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Digital map or image, location metadata and phylogenetic trees
Output data Images and analysis files
Operating system Mac OS, Windows
Programming languages C++, Python
License GNU General Public License version 2.0
Computer skills Medium
Version 2.4.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Rob Beiko <>

Publications for GenGIS

GenGIS in pipelines

 (3)
2017
PMCID: 5440521
PMID: 28588568
DOI: 10.3389/fmicb.2017.00909

[…] include the microreact system for phylogeographic analysis of snv or mlst data (), the phyloviz system (; ) for epidemiological analysis and visualization of sequence (snv and mlst) data, and gengis (, ), which allows the overlay and analysis of phylogenetic data and associated metadata on digital maps., as mentioned above, the gmi:mdm standard (developed by the gmi and adopted […]

2014
PMCID: 4079597
PMID: 24987846
DOI: 10.1371/journal.pone.0101108

[…] to exploit its capacity for the visualization of large trees. in two cases where dna barcode analysis suggested potential cases of overlooked diversity, we also generated “geo-phylogenies” using gengis 2.2.0 to better visualize the geographical structure of genetic variation. mega 5.2.2 was also used to produce character-based trees using the maximum parsimony (mp) criterion (all settings […]

2013
PMCID: 3779339
PMID: 24026825
DOI: 10.1098/rspb.2013.1910

[…] was assessed in tracer []. a median-joining network was constructed using phylonet5 v. 1.0.0 (a. helgason 2009, unpublished). changes in phylogeographic patterns over time were visualized in gengis []., serial coalescent simulations were run with bayesian serial simcoal [] and analysed in an approximate bayesian computation (abc) framework [] using the abc package in r []. summary […]


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GenGIS in publications

 (22)
PMCID: 5929190
PMID: 29313474
DOI: 10.4269/ajtmh.17-0441

[…] map as a location-finding overlay, the culture-positive cases were plotted by place of residence at the time of diagnosis. geographic information system analysis of genotype data was performed using gengis v2·5·0 (http://kiwi.cs.dal.ca/gengis/download) and r v3·3·2 (https://www.r-project.org/)., the maximum likelihood tree was projected onto an administrative boundary vector map layer of sri […]

PMCID: 5660214
PMID: 29079830
DOI: 10.1038/s41598-017-14738-6

[…] of a. paeoniifolius (16 samples) and 5 populations of the cultivar a. paeoniifolius ‘yellow’ (20 samples) were collected in 2016. a map of the sampling locations was created using software gengis 2.5.0 (http://kiwi.cs.dal.ca/gengis/main_page) and free raster map data from natural earth (http://www.naturalearthdata.com/) (fig.  and table ). leaves were randomly selected […]

PMCID: 5507994
PMID: 28751882
DOI: 10.3389/fmicb.2017.01313

[…] and east arm. bootstrap analysis was conducted on 500 rarefied trees. the tree and median bacterial taxa information at family level were combined with a geo-referenced map from darwin harbour in gengis 2.4.0. the map was georeferenced in arcmap 10.1 (www.esri.com) using shapefiles obtained from the northern territory government., to find bacterial families significantly associated […]

PMCID: 5496553
PMID: 28690819
DOI: 10.1002/ece3.3036

[…] chloroplast sequence data by constructing a parsimony network (clement, posada, & crandall, ; templeton, crandall, & sing, ) in popart (http://popart.otago.ac.nz, june 2016). we also used gengis 2.1.1 (parks et al., ) to visualize plastid and nuclear sequence geographic distributions., to assess levels of genetic divergence between putative taxonomic species and a priori defined […]

PMCID: 5477509
PMID: 28537247
DOI: 10.1038/ncomms15323

[…] representative geographically locations or provinces in china (liaoning, ningxia, jiangsu and guangdong) where rice fields are seriously harmed by weedy rice. the geographic map was plotted using gengis v2 (ref. ). the 76 cultivated rice including local landraces and cultivars planted in recent 30 years in the four regions. liaoning and ningxia locate in northern china which temperate […]


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GenGIS institution(s)
Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
GenGIS funding source(s)
Genome Canada, Genome Atlantic, NSERC, CIHR, Killam Trusts, Canada Research Chairs

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