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CONDENSED CODON MATRIX: Ranking codons and orthologs based on their phylogenetic signal
scoreCharactersOnTree.py
Created By: Justin Miller
Email: jmiller@byu.edu

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Purpose: Determine which codon usages and aversions display the strongest phylogenetic signals.


ARGUMENT OPTIONS:

	-h, --help     show this help message and exit
	-o OUTPUT      Output File
	-r REF         Path to the Reference Phylogeny in Newick Format
	-c CHAR        Path to Character File


REQUIREMENTS:

scoreCharactersOnTree.py uses Python version 2.7

Python libraries that must be installed include:
1. sys
2. argparse
3. re
4. regex
5. pyparsing

If any of those libraries is not currently in your Python Path, use the following command:
pip install --user [library_name]
to install the library to your path.


Input Files:
This algorithm requires two input files: a reference phylogeny and a character file (see test files for examples).
An output file is optional. If not provided, output will be written to standard out.

Output File:
An output file is not required. If an output file is not supplied, the number of independent origins will be written to standard out.


USAGE:

Typical usage requires the -c and -r options with the optional -o. 


Example usage:
python scoreCharactersOnTree.py -c test/character.txt -r test.nwk -o output
python scoreCharactersOnTree.py -c test/character.txt -r test.nwk > output


Running one of the above commands will produce a single output called output in the current directory.
This command should be fast. 

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Thank you, and happy researching!!