Location information and metadata: We will use a couple of different representations of the data. For more detailed manipulations, I usually fire up QGIS. GenGIS has the MapMaker tool ( ) which allows you to export a subsection of three really nice Natural Earth raster maps at a specified resolution.

The map data we will use today are sourced from Natural Earth. The USGS Earth Explorer has some very useful data, but (i) You’ll need a login, and (ii) GenGIS may gak on some of the larger datasets. Natural Earth has beautiful raster and vector data files that interact easily with GenGIS unfortunately dynamic ranges are not available. If you want Canadian data, you can try NRCan although the data cannot be downloaded immediately. However, there is nothing like digital maps to send you on circular Web page trips (well, maybe the SRA comes close). If you can find it, it’s pretty much assured you can load it. The good news is that by making use of the ***GDAL libraries, GenGIS supports a large number of geographic file formats (GeoTIFF, ASCIIGrid, PNG, ESRI shapefiles, etc.). GenGIS requires you to load in a map file, which is less easy. Maps: Microreact uses Leaflet.js to connect to OpenStreetMap maps, which is easy. I compiled a tree, information about locations, and specific isolates into a set of files that we will use in the examples below. Since the Haiti sequences constituted a clade that was embedded within a larger Nepalese clade, the authors concluded that Nepalese peacekeepers were the most likely source of the epidemic strain: this corroborated with the geographic proximity of peacekeeping camps with affected areas. (2014), which used phylogenetic methods to identify the most probably source for the introduction of Vibrio cholerae into Haiti. The dataset we will be using is adapted from Eppinger et al. Export a Microreact project and create visualizations in GenGIS.Create a Microreact project and use it for outbreak investigation.Build a simple tree visualization using Phylocanvas.Infectious Disease Genomic Epidemiology Phylogeography Lab Phylogeography CBW tutorial Rob Beiko - May 1, 2017īy the end of the tutorial, you will be able to:

Labelview 2015 tutorial