GPT TUTORIAL

What is GPT?

GPT (Global Positioning Trees) is a web-server that maps phylogenetic trees on a virtual globe. This server has been designed to be an easy-to-use tool to track evolutionary processes and will be useful for phylogeographical and epidemiological studies. The GPT server minimally requires a phylogenetic tree and geographical coordinates of species to display the tree topology on Google Earth.

How to cite: Puigbo P. (2012) GPT: Global Positioning Trees. http://ppuigbo.me/programs/GPT

How to use GPT? (minimal requirements)

    Step 1) Insert a phylogenetic tree.
    Step 2) Insert Geographical coordinates of species.
    Step 3) Press 'Make KML' to generate a KML file to be opened on Google Earth.

Examples

    Example 1 - Phylogenetic tree + Geographical coordinates
    Example 2 - Phylogenetic tree + Geographical coordinates + Description of species
    Example 3 - Geographical coordinates + Timestamp
    Example 4 - Geographical areas
    Example 5 - Phylogenetic tree + Geographical coordinates + Small scale
    Example 6 - GPS track

Phylogenetic tree format

    Just topology: (((AA,BB),(CC,DD)),EE);      ('Topology' checkbox must be checked)
    Topology + Branch Lengths: (((AA:1.0,BB:2.0):0.87,(CC:2.2,DD:2.9):0.5):0.46,EE:4.2);      (Both 'Topology' and 'Branch lengths' checkboxes must be checked)
    Topology + Branch lengths + Bootstrap values: (((AA:1.0,BB:2.0)85:0.87,(CC:2.2,DD:2.9)92:0.5):0.46,EE:4.2);      (Both 'Topology' and 'Branch lengths' checkboxes must be checked. Bootstrap values will not be considered and will be removed from the tree)

* The 'Title' box is optional and may contain only alphanumerical characters.

Geographical coordinates format

     Species1(Latitude,Longitude)
     Species2(Latitude,Longitude)
     ...
     SpeciesN(Latitude,Longitude)

    Example:
     AA(41.46826580,2.22612210)
     BB(41.16695420,1.37522490)
     CC(42.5462450,1.6015540)
     DD(43.391160,5.5323519)
     EE(48.9021450,2.46992090)

* Insertion of geographical coordinates without a tree will only map the distribution of species on the virtual globe

Timestamp in coordinated universal time format.
    Example:
     Alabama(2012-01-01T21:05:02Z)
     Alaska(2012-01-02T21:05:02Z)
     Arizona(2012-01-03T21:05:02Z)
     Arkansas(2012-01-04T21:05:02Z)
     Iowa(2012-01-04T21:05:02Z)

GPS track format

     Species1(Time,Latitude,Longitude,Altitude)
     Species1(Time,Latitude,Longitude,Altitude)
     ...
     Species2(Time,Latitude,Longitude,Altitude)
     Species2(Time,Latitude,Longitude,Altitude)
     ...

    Example:
     A(2010-05-28T02:02:09Z,-122.207881,37.371915,156)
     A(2010-05-28T02:02:35Z,-122.205712,37.373288,152)
     A(2010-05-28T02:02:44Z,-122.204678,37.373939,147)
     A(2010-05-28T02:02:53Z,-122.203572,37.37463,142.199997)
     A(2010-05-28T02:02:54Z,-122.203451,37.374706,141.800003)
     A(2010-05-28T02:02:55Z,-122.203329,37.37478,141.199997)
     A(2010-05-28T02:02:56Z,-122.203207,37.374857,140.199997)
     B(2010-05-28T02:02:09Z,-122.207881,37.371915,156)
     B(2010-05-28T02:02:35Z,-122.205712,37.39,152)
     B(2010-05-28T02:02:44Z,-122.204678,37.39,147)
     B(2010-05-28T02:02:53Z,-122.203572,37.4,142.199997)
     B(2010-05-28T02:02:54Z,-122.203451,37.41,141.800003)
     B(2010-05-28T02:02:55Z,-122.203329,37.42,141.199997)
     B(2010-05-28T02:02:56Z,-122.203207,37.43,140.199997)

3D bargraphs format

     Species1(Width,TransparencyCode,Color,Latitude,Longitude,Altitude)
     Species1(Width,TransparencyCode,Color,Latitude,Longitude,Altitude)
     ...
     Species2(Width,TransparencyCode,Color,Latitude,Longitude,Altitude)
     Species2(Width,TransparencyCode,Color,Latitude,Longitude,Altitude)
     ...

    Example:
     A(1.5,50,blue,-86.9175799283,32.6641560879,100000)
     A(1.5,50,blue,-86.7158863338,32.6618217133,100000)
     A(1.5,50,blue,-86.7140703779,32.7056948343,100000)
     A(1.5,50,blue,-86.4131291141,32.7073727247,100000)
     A(1.5,50,blue,-86.4111843301,32.4099430401,100000)
     A(1.5,50,blue,-86.4967766143,32.3444500625,100000)
     A(1.5,50,blue,-86.7172361055,32.4025734658,100000)
     A(1.5,50,blue,-86.8149068513,32.340820721,100000)
     A(1.5,50,blue,-86.8904950767,32.5027898516,100000)
     A(1.5,50,blue,-86.9175799283,32.6641560879,100000)

Description format

     Species1(Description_of_species_1)
     Species2(Description_of_species_2)
     ...
     SpeciesN(Description_of_species_N)

    Example:
     AA(Description_of_species_AA)
     BB(Description_of_species_BB)
     CC(Description_of_species_CC)
     DD(Description_of_species_DD)
     EE(Description_of_species_EE)

* Desription of species is optional and may contain only alphanumerical characters or underscore.

Style

     - Scale: this parameter converts branch lengths to altitude. Default: 100000.
     - Ground: this parameter assures that lines will not be underground when crossing the globe. Default: 5.
     - Tips color: the tips of the tree will be shown in blue by default (see below for other available colors).
     - Topology color: the tree topology will be shown in red by default (see below for other available colors).
     - Width: the width of both topology and tips is set to 5.
     - Width: the width of both topology and tips is set to 5.
     - Other available colors: