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README

     PSAR (Probabilistic Sampling-based Alignment Reliability) Score
     ===============================================================

1. How to compile?
------------------
	
	You just need to type: make

2. How to run?
--------------
	
	psar <alignment fasta file> <parameter file> <output directory> [-s <sampling threshold>] [-p]

	- Alignment fasta file: input alignment file in FASTA format

	- Parameter file: additional parameters 
	
	- Output directory: directory for storing sampled alignments
	
	- -s <Sampling threshold> (optional)
		- Parameter to control the degree of sampling
		- Should be in range [0,1]
		- Lower value produces alignment samples more close to 
				the optimal alignment
	
	- -p: Print estimated parameters (optional)

	Example: ./psar example/test.fa example/parameters.txt example/test

3. What are produced?
---------------------

	PSAR_pair.txt: PSAR pair scores
	PSAR_column.txt: PSAR column scores
 
	Sampled alignments are stored in the given output directory.

4. How to ask questions?
------------------------

	Contact Jaebum Kim (jkim63@illinois.edu)	

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