SPEL: specificity determinants by log-likelihood ratios

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Requirements:
1) servers with multiple CPUs or linux clusters
2) already installed MPICH package with mpiCC or mpicxx compiler


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Install SPEL:
1) un-tar the package:
	tar xvf SPEL.tar
2) go to directory SPEL
3) run the following script:
	perl make_spel.pl
4) go to directory src/, run the following commands:
	make clean
	make

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How to use this package?
There is a perl file, SPEL.pl, which link all programs.
Usage: perl SPEL.pl alignment_file [-cpu n]
alignment_file: plain alignment not ClustalW file format
optional parameters:
	CPU number: 'n' after '-cpu' should be a positive integer
	CPU number should not be less than the number of 
		positions (sites) in the alignment

Note: the bin directory name in SPEL.pl ($command_dir) should be changed accordingly

Alignment format: plain format or clustal format
alignment example:
format 1:
1234  AAAAAA
2345  BBBBBB
3456  CCCCCC
4567  DDDDDD

format 2:
1234  AAAAAA
2345  BBBBBB
3456  CCCCCC
4567  DDDDDD

1234  EEEE
2345  FFFF
3456  GGGG
4567  HHHH

Output: output file is alignment_file.specificity. The sites are 
ordered by the inferred importance of functional specificity.
