README.txt

Suppmlementary Information for:

    Fossil evidence for the pharyngeal origin of the vertebrate pectoral girdle

    Authors:
    Martin D Brazeau, Marco Castiello, Amin El Fassi El Fehri, 
    Louis Hamilton, Alexander O Ivanov, Zerina Johanson, Matt Friedman


This folder contains all of the necessary files for running the phylogenetic analysis used 
in this paper. We used TNT (version 1.6: see Methods references), but the data and script have 
been tested with version 1.5.

Rerunning the analyses:
The best approach is to open TNT and change the working directory to this folder's location. 
If you're using the command-driven version of TNT this is as simple as using the command:

    cdir /path/to/Phylogenetic_analysis_files;

where the "path/to" part is replaced with the actual path on your computer. To save having to
type out the whole path, on most systems, simply dragging and dropping the relevant folder 
into the terminal window after typing in the "cdir" command will automatically fill it in.

After changing the working directory, simply run the command:

    run tntsets.run;

This will run both the standard and implied weights searches and export a Nexus-formatted file 
containing both trees.

NOTE 1: The script will generate a temporary tree file (ttemp.tre) which you should delete from
the working directory if you want to run the script again.

NOTE 2: Individual systems will vary. Depending on availability of memory on your computer, 
you might need to change the `mxram` value in the script to a lower number.
