README phyloGenerator
Will Pearse (will.pearse@gmail.com)
This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.

Automated phylogeny generation for ecologists.

EASY USE:
* Download a pre-packaged binary for whatever system you're on (Mac, Windows)
* Mac: Open Terminal, run the file 'phyloGenerator.app/Contents/MacOS/phyloGenerator' - note that double clicking it will generate an error! For example, if I'd installed phyloGenerator into my home directory, I'd type '/Users/will/phyloGenerator.app/Contents/MacOS/phyloGenerator'.
* PC: Either double-click 'phyloGenerator.exe', or open up command prompt, change directory (cd) into the 'phyloGenerator' directory and type 'phyloGenerator.exe'. This way when the program finishes you'll still have all the messages it generates on screen.
* Linux: No easy-use, sorry! Follow the instructions below for 'compiling' it.

'COMPILING' IT:
Short answer: Install Python >=2.6; Numpy and SciPy for Python; Biopython >=2.5. Set up a folder ('requires') in the same folder as 'phyloGenerator.py' that contains the programs you'll use - check http://willpearse.github.com/phyloGenerator/install.html#compiling for the names of the programs.
Long answer: go to http://willpearse.github.com/phyloGenerator/install.html

EXAMPLES:
There should be a 'Demos' folder with your distribution - if not, *please email me*. Inside each folder there's either a file called 'demo.txt' or 'demo.sh' - open whichever one you have. Have a look at 'Silwood_Plants' first. There're walkthrough videos online (http://willpearse.github.com/phyloGenerator/guide.html#screencasts).

QUESTIONS:
Please feel free to drop me an email, or put any feature requests/bugs online at https://github.com/willpearse/phyloGenerator/issues.

CITATION:
Currently, this is under review, so contact me for citation information.

I hope you enjoy phyloGenerator!

Will Pearse (will.pearse@gmail.com)