This application was tested extensively using Mozilla Firefox. To ensure compatibility consider switching.

Preparation

There are several things you need before you begin the creation process:

1) Make sure that javascript is enabled in your browser.

2) (Optional) Download and install the google earth browser plugin. You can get it here.

3) Create a routemap account: register here.

4) Download TNT analysis for trees and character evolution: available here.

5) Make two input files: Download Samples

Sequence datafile - a fasta file containing phylogenetic data, such as DNA sequences.
Geographic datafile - a comma separated (csv) file containing a list of each taxon, followed by a location name, latitude, and longitude. The first line of the file must be a header similar to that found in the sample file.
NOTE: TNT limits the number of unique placenames to 31, and placenames cannot contain spaces.

Once these steps are completed, click 'New Kml' at the top of the page to begin the creation process.

Advanced Options

Outgroup: Specify an outgroup. By default, the first taxa in the fasta is used.

Search level: The search level. Higher level = more thorough search, but slower.

Treelength to hit: The length of the most parsimonious trees if you know it. This could speed up the tree collection.

Hits to minimum length: The number of independent hits to minimum length during search.

Load trees from file: Load trees from a treefile instead of performing a search. Trees needs to be in a format readble by tnt. To use this option, specify the filename of the treefile. When you run the downloaded tntscript, make sure the specified treefile is present in the same folder as the script.

Save trees to file: Save the trees found during search to a file.

Custom search parameters: Replace the search parameters with custom commands. Completely replaces the xm= line in the tnt script.

Analyzing results

For new-style Kmls: Click the dot for a location of interest. Mouse over the dots that arise from your location of interest to see incoming and outgoing transmissions. On mouse over, the green lines represent outgoing routes for spread of H1N1; red lines represent incoming routes for spread of H1N1.

For old-style Kmls: Bidirectional transmissions are represented by yellow lines. Unidirectional transmissions are either green (outgoing) or red (incoming). Because Google Earth does not allow directional lines, the only way to ascertain the direction of unidirectional transmissions is to view the transmission descriptions in the folder struction under "Temporary Places."