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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

Versioning


No version available

Maintainer


  • person_outline Rob Beiko

Publications for GenGIS

GenGIS citations

 (34)
library_books

Exploring the genetic and adaptive diversity of a pan Mediterranean crop wild relative: narrow leafed lupin

2018
PMCID: 5852200
PMID: 29353413
DOI: 10.1007/s00122-017-3045-7

[…] timum K was obtained using the algorithm implemented in fastSTRUCTURE to choose model complexity (Raj et al. ). To understand the relationship between phylogeny and geographical distribution, we used GenGIS 2.4.0 (Parks et al. ). The unrooted distance-based phylogeny tree, which was implemented as Newick format in GenGIS, was obtained using Neighbor Joining method within the NEIGHBOR package in PH […]

call_split

Clinical, Bacteriologic, and Geographic Stratification of Melioidosis Emerges from the Sri Lankan National Surveillance Program

2018
PMCID: 5929190
PMID: 29313474
DOI: 10.4269/ajtmh.17-0441
call_split See protocol

[…] 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 Lank […]

library_books

Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD seq

2017
Sci Rep
PMCID: 5660214
PMID: 29079830
DOI: 10.1038/s41598-017-14738-6

[…] opulations 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 from each populat […]

library_books

Spatial and Temporal Microbial Patterns in a Tropical Macrotidal Estuary Subject to Urbanization

2017
Front Microbiol
PMCID: 5507994
PMID: 28751882
DOI: 10.3389/fmicb.2017.01313

[…] Bay 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. […]

call_split

Molecular genetic analysis of two native desert palm genera, Washingtonia and Brahea, from the Baja California Peninsula and Guadalupe Island

2017
Ecol Evol
PMCID: 5496553
PMID: 28690819
DOI: 10.1002/ece3.3036
call_split See protocol

[…] nuclear and 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 geograph […]

library_books

Genomic variation associated with local adaptation of weedy rice during de domestication

2017
Nat Commun
PMCID: 5477509
PMID: 28537247
DOI: 10.1038/ncomms15323

[…] our 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 japonica […]

Citations

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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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