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Google Earth files for avian flu virus
The Google Earth file that accompanies the paper "Genomic Analysis and Geographic Visualization of the Spread of Avian Influenza (H5N1)" (Janies et al., doi:10.1080/10635150701266848, or OpenURL) is available here (aiTrees.kmz).
The paper has received some media coverage. Click on the image (or here) to see a news item from CBS Denver.
README for the aiTrees.kmz
The file aiTrees.kmz is meant to be opened with Google Earth version 4.x.x. The file can be opened with earlier versions of Google Earth, but will not be fully functional and in some cases wont display at all. Google Earth can be downloaded at: http://earth.google.com/download-earth.html
After installing Google Earth, the file type .kmz will be associated with the Google Earth application, and simply double-clicking the file will open it properly.
When Google Earth loads the aiTrees.kmz file all the data from our file will be in the 'Places' frame on the left hand side of the screen. A folder 'aiTrees.kml' should be expanded with four sub-folders; 'Lys-627', 'Host Order', 'node calculation', and 'credits'. By default the 'credits' folder is selected for display. Clicking the radio button beside either of the other folders will load its contents.
If you click on the radio button beside "Host Order" two legends will load on the screen as well as the tree. At the top of the screen will be a time slider, by moving slider forward in time you will see the geographic expansion of the phylogenetic tree. Within the "Tree" sub-folder of "Host Order" you will find each isolate and Hypothetical Taxonomic Unit (HTU) from our phylogenetic hypothesis. By double clicking on each isolate or HTU icon you will be presented with a pop-up window of diagnositic mutations for that clade.
If you click the radio button beside 'Lys-627', two legends will load on the screen as well as the tree. At the top of the screen will be a time slider, by moving slider forward in time you will see the geographic expansion of the phylogenetic tree. Within the 'Tree' sub-folder of 'Lys-627' you will find each isolate and Hypothetical Taxonomic Unit (HTU) from our phylogenetic hypothesis.
In any view, by double clicking on an isolate of interest or using the zoom tool you can focus on certain geographic areas. There are many more functions so take your time to explore the tree and don't hesitate to ask us questions.
Another great avian flu occurance data + Google Earth project is one by Declan Butler descrfibed on his blog:
The Barcode of Life
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution