README

**Install***
Install python 2.x (tested on 2.5-2.7)
Unzip the files in the desired directory

***Required python libraries***
numpy
csv

***Generate dataset***
The instructions on how to obtain the files species.txt and homologs.txt are detailed here:
http://evolutionarygenomics.imim.es/josepl/codeigniter/index.php/pages/view/how_files
It's very important to name the files species.txt and homologs.txt

***Run***
Once you've gathered the 2 required files for your dataset put them in the 'files' directory and run the palo script from the command line with:
> python palo2.py

You will find the output of the script in the 'files' folder.

***Tips***
The files folder contains an example dataset (species.txt and homologs.txt).
You can modify the folder containing the files by changing the folder variable in palo2.py (line 5)