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README

     PSARAlign
     =========

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

2. Requirement
--------------

	Perl should be installed in your system (http://www.perl.org/get.html)

2. How to run?
--------------
	
	PSARAlign.pl <alignment fasta file> <parameter file> <output directory>

	- Alignment fasta file: input alignment file in FASTA format

	- Parameter file: additional parameters for the PSAR program 
	
	- Output directory: directory for storing output 
	
	Example: ./PSARAlign.pl example/test.fa example/parameters.txt myout 

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

	- revised.aln.fa: revised alignment by PSARAlign
	
	- PSAR_pair.txt: PSAR pair scores
	
	- PSAR_column.txt: PSAR column scores
 
	- Sampled alignments will be stored in a "samples" subdirectory 
	in the given output directory.

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

	Contact Jaebum Kim (jbkim@konkuk.ac.kr)	

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