Google Earth

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BEAST Documentation->Tutorials-> Google Earth

Visualizing phylogeographies in Google Earth

This tutorial describes how to convert a location-annotated MCC to KML for visualization in Google Earth. The tutorial uses the MCC tree generated in Tree summary. For KML conversion, download the phylogeo.jar. To map the MCC tree in Google Earth, we have to associate each location with a particular latitude and longitude. To this purpose, prepare a tab-delimited file including each location, its latitude and longitude. For the H5N1 example, this should look like this:

Fujian	25.917	118.283
Guangdong	22.87	113.483
Guangxi	23.6417	108.1
Hebei	39.3583	116.6417
Henan	33.875	113.5
HongKong	22.3	114.167
Hunan	27.383	111.517

To list the options of the KML conversion tool, run phylogeo using the help option:

java -jar phylogeo.jar -help

Many options allow setting the style of the branch mapping. For our purposes, we can use:

java -jar phylogeo.jar -coordinates locationCoordinates -annotation states -mrsd 2005.5 -radius 50000 H5N1_HA_discrete_MCC.tre output.kml

where "-coordinates" specifies the file to which we saved the locations and their coordinates, "-annotation" specifies the string by which the states are annotated in the trees (an older BEAST version used "state" instead of "states"), "-mrsd" specifies the most recent sampling date, "-radius" sets the radius of the circles that represent the number of lineages maintaining a particular state. The last two arguments specify the input and output file.

Open the output file in Google Earth; a time bar indicating the time scale of the tree should appear in the upper left corner. Clicking the clock/play button starts an animation of the diffusion through time. The final tree mapping should look like this:

For more information about the options for KML conversion and bug reporting, contact philippe.lemey (at) gmail.com.